I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 19 05:50:37 +14 2023 I: pbuilder-time-stamp: 1681833037 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [canu_2.0+dfsg-2.dsc] I: copying [./canu_2.0+dfsg.orig.tar.xz] I: copying [./canu_2.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 29 10:38:47 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./canu_2.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting canu in canu-2.0+dfsg dpkg-source: info: unpacking canu_2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking canu_2.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-mhap-at-runtime.patch dpkg-source: info: applying external-mhap.patch dpkg-source: info: applying canu_version.patch dpkg-source: info: applying remove-deprecated-sysctl.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 19 05:51 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=370855793108475db7725c07eb13bc37 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=30765 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wupB1E94/pbuilderrc_3yG5 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wupB1E94/b2 --logfile b2/build.log --extrapackages usrmerge canu_2.0+dfsg-2.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 10:21 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:21 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 19 05:51 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/30765/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libmeryl-dev; however: Package libmeryl-dev is not installed. pbuilder-satisfydepends-dummy depends on libfilesys-df-perl; however: Package libfilesys-df-perl is not installed. pbuilder-satisfydepends-dummy depends on mhap; however: Package mhap is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fastjar{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jaligner{a} jarwrapper{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcommons-compress-java{a} libcommons-parent-java{a} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libelf1{a} liberror-prone-java{a} libexpat1{a} libfastutil-java{a} libfile-stripnondeterminism-perl{a} libfilesys-df-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgraphite2-3{a} libguava-java{a} libharfbuzz0b{a} libicu72{a} libjpeg62-turbo{a} libjsr305-java{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmeryl-dev{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libssw-java{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mhap{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 76 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After unpacking 448 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 binfmt-support i386 2.2.2-2 [65.5 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.8-1 [1412 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 java-common all 0.74 [6388 B] Get: 20 http://deb.debian.org/debian bookworm/main i386 libavahi-common-data i386 0.8-9 [107 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 libavahi-common3 i386 0.8-9 [43.3 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libdbus-1-3 i386 1.14.6-1 [213 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libavahi-client3 i386 0.8-9 [47.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libcups2 i386 2.4.2-3 [261 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-4 [410 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libnspr4 i386 2:4.35-1 [123 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libnss3 i386 2:3.87.1-1 [1439 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libasound2-data all 1.2.8-1 [20.5 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libasound2 i386 1.2.8-1+b1 [388 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libpcsclite1 i386 1.9.9-2 [50.9 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 openjdk-17-jre-headless i386 17.0.6+10-1 [42.2 MB] Get: 43 http://deb.debian.org/debian bookworm/main i386 default-jre-headless i386 2:1.17-74 [2932 B] Get: 44 http://deb.debian.org/debian bookworm/main i386 ca-certificates-java all 20230103 [11.4 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 50 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 52 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 fastjar i386 2:0.98-7 [47.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 jaligner all 1.0+dfsg-10 [132 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 jarwrapper all 0.78 [21.8 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 64 http://deb.debian.org/debian bookworm/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 65 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-20 [9510 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 67 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libcommons-compress-java all 1.22-1 [615 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libguava-java all 31.1-1 [2613 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libfilesys-df-perl i386 0.92-7+b1 [11.4 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libmeryl-dev i386 0~20150903+r2013-8+b3 [72.6 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libssw-java i386 1.1-13 [23.9 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 mhap all 2.1.3+dfsg-3 [160 kB] Fetched 105 MB in 4s (27.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../00-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../01-binfmt-support_2.2.2-2_i386.deb ... Unpacking binfmt-support (2.2.2-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... 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Unpacking mhap (2.1.3+dfsg-3) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up fastjar (2:0.98-7) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up liblcms2-2:i386 (2.14-2) ... Setting up libfastutil-java (8.5.11+dfsg-1) ... Setting up libboost1.74-dev:i386 (1.74.0+ds1-20) ... Setting up libicu72:i386 (72.1-3) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up java-common (0.74) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.74.6-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libfilesys-df-perl (0.92-7+b1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libssw-java (1.1-13) ... Setting up libasound2-data (1.2.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2) ... Setting up libnspr4:i386 (2:4.35-1) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:i386 (0.8-9) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:i386 (1.14.6-1) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up libmeryl-dev (0~20150903+r2013-8+b3) ... Setting up autopoint (0.21-12) ... Setting up binfmt-support (2.2.2-2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up fonts-dejavu-core (2.37-6) ... Setting up libpcsclite1:i386 (1.9.9-2) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libasound2:i386 (1.2.8-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up openssl (3.0.8-1) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up jarwrapper (0.78) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:i386 (0.8-9) ... Setting up libnss3:i386 (2:3.87.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:i386 (2.12.1+dfsg-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libavahi-client3:i386 (0.8-9) ... Setting up libcommons-compress-java (1.22-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcups2:i386 (2.4.2-3) ... Setting up debhelper (13.11.4) ... Setting up openjdk-17-jre-headless:i386 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up jaligner (1.0+dfsg-10) ... Setting up libguava-java (31.1-1) ... Setting up mhap (2.1.3+dfsg-3) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/30765/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/30765/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/canu-2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../canu_2.0+dfsg-2_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --sourcedirectory=src/ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/canu-2.0+dfsg' rm -rf Linux-* rm -f src/canu_version.H make[1]: Leaving directory '/build/canu-2.0+dfsg' dh_autoreconf_clean -O--sourcedirectory=src/ dh_clean -O--sourcedirectory=src/ debian/rules build dh build --sourcedirectory=src/ dh_update_autotools_config -O--sourcedirectory=src/ dh_autoreconf -O--sourcedirectory=src/ dh_auto_configure -O--sourcedirectory=src/ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-2.0+dfsg' dh_auto_build cd src && make -j7 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/canu-2.0+dfsg/src' WARNING: WARNING: g++ 12 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: Building for 'Linux' '5.10.0-21-686-pae' as 'i686' into '/build/canu-2.0+dfsg/Linux-i686/{bin,obj}'. Using '/usr/bin/g++' version '12'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'. Building release v2.0 g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/edlib.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-buffered.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-compressed.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/files-memoryMapped.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/logging.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/strings.C utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': utility/files-memoryMapped.C:76:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | read(_fd, _data, _length); | ~~~~^~~~~~~~~~~~~~~~~~~~~ utility/files-memoryMapped.C: In destructor 'memoryMappedFile::~memoryMappedFile()': utility/files-memoryMapped.C:102:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | write(_fd, _data, _length), close(_fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ utility/files.C: In function 'void writeToFile(void*, const char*, uint64, uint64, FILE*)': utility/files.C:89:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:89:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:89:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 89 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 90 | nWritten, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:94:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n", | ~~^ | | | long unsigned int | %llu 95 | nWritten, nObjects, description, objectSize), exit(1); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:94:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n", | ~~^ | | | long unsigned int | %llu 95 | nWritten, nObjects, description, objectSize), exit(1); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:94:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 94 | fprintf(stderr, "writeToFile()-- After writing %lu out of %lu '%s' objects (%lu bytes each): Short write\n", | ~~^ | | | long unsigned int | %llu 95 | nWritten, nObjects, description, objectSize), exit(1); | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C: In function 'uint64 loadFromFile(void*, const char*, uint64, uint64, FILE*, bool)': utility/files.C:134:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n", | ~~^ | | | long unsigned int | %llu 135 | nLoaded, nObjects, description, objectSize); | ~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:134:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n", | ~~^ | | | long unsigned int | %llu 135 | nLoaded, nObjects, description, objectSize); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:134:88: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): End of file\n", | ~~^ | | | long unsigned int | %llu 135 | nLoaded, nObjects, description, objectSize); | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:150:57: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:150:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/files.C:150:86: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 150 | fprintf(stderr, "loadFromFile()-- After loading %lu out of %lu '%s' objects (%lu bytes each): %s\n", | ~~^ | | | long unsigned int | %llu 151 | nLoaded, nObjects, description, objectSize, strerror(errno)), exit(1); | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system.C utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:160:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from utility/logging.H:29, from utility/logging.C:26: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::rotate()' at utility/logging.C:160:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:161:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 161 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::rotate()' at utility/logging.C:161:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::rotate()' at utility/logging.C:157:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 8205 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/logging.C: In member function 'void logFileInstance::rotate()': utility/logging.C:158:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); | ^ utility/logging.C:158:43: note: using the range [-2147483648, 2147483647] for directive argument 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::rotate()' at utility/logging.C:158:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 13 and 8220 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::rotateMessage()' at utility/logging.C:173:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: warning: 'int __builtin___snprintf_chk(char*, unsigned int, int, unsigned int, const char*, ...)' specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': utility/files.C:311:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 311 | symlink(pathToFile, pathToLink); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ utility/files.C: In function 'void AS_UTL_loadFileList(char*, std::vector&)': utility/files.C:678:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 678 | fgets(line, FILENAME_MAX, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ utility/files.C:684:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 684 | fgets(line, FILENAME_MAX, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/system-stackTrace.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sequence.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-reader.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-block.C utility/kmers-writer.C:58:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] 58 | #warning how to set prefix size for streaming operations? | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-writer-stream.C In file included from utility/kmers.H:32, from utility/kmers.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-statistics.C In file included from utility/kmers.H:32, from utility/kmers-reader.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/kmers-reader.C:208:46: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); | ~~~~~^ ~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers-reader.C:208:52: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 208 | fprintf(stderr, " magic 0x%016lx%016lx '%s'\n", m1, m2, m); | ~~~~~^ ~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers-reader.C: In function 'void dumpMerylDataFile(char*)': utility/kmers-reader.C:342:29: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~^ | | | long unsigned int | %8llu 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:55: warning: format '%lx' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); | ~~ | | | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:68: warning: format '%lx' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); | ~~ | | | uint64 {aka long long unsigned int} utility/kmers-reader.C:342:77: warning: format '%lx' expects argument of type 'long unsigned int', but argument 11 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 342 | fprintf(stdout, "0x%016lx %8lu %5u %5u %5u 0x%016lx %5u 0x%016lx 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 343 | prefix, nKmers, kCode, unaryBits, binaryBits, k1, cCode, c1, c2); | ~~ | | | uint64 {aka long long unsigned int} In file included from utility/kmers.H:32, from utility/kmers-writer-stream.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} In file included from utility/kmers.H:32, from utility/kmers-writer.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from utility/kmers.H:32, from utility/kmers-statistics.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from utility/kmers.H:32, from utility/kmers-writer-block.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/kmers-exact.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-writer.C: In member function 'void kmerCountFileWriter::initialize(uint32, bool)': utility/kmers-writer.C:78:117: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 78 | fprintf(stderr, "kmerCountFileWriter()-- Creating '%s' for %u-mers, with prefixSize %u suffixSize %u numFiles %lu\n", | ~~^ | | | long unsigned int | %llu 79 | _outName, (_prefixSize + _suffixSize) / 2, _prefixSize, _suffixSize, _numFiles); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-writer.C: In member function 'uint32 kmerCountFileWriter::fileNumber(uint64)': utility/kmers-writer.C:169:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-writer.C:169:98: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 169 | fprintf(stderr, "kmerCountFileWriter()-- Formed invalid file number %lu >= number of files %lu:\n", oi, _numFiles); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/kmers-writer.C:170:71: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 170 | fprintf(stderr, "kmerCountFileWriter()-- prefix 0x%016lx\n", prefix); | ~~~~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-writer-block.C: In member function 'void kmerCountBlockWriter::mergeBatches(uint32)': utility/kmers-writer-block.C:325:84: warning: format '%lx' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 326 | oi, ii, prefix, inBlocks[ii].prefix()); | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-writer-block.C:325:96: warning: format '%lx' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 325 | fprintf(stderr, "ERROR: File %u segments 1 and %u differ in prefix: 0x%016lx vs 0x%016lx\n", | ~~~~~^ | | | long unsigned int | %016llx 326 | oi, ii, prefix, inBlocks[ii].prefix()); | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-writer-block.C:370:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); | ~~^ ~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-writer-block.C:370:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 370 | fprintf(stderr, "savnKmers %lu > nKmersMax %lu\n", savnKmers, nKmersMax); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/kmers-reader.C: In member function 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/kmers-reader.C:143:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 143 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from utility/kmers.H:29: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void kmerCountFileReader::initializeFromMasterIndex(bool, bool, bool)' at utility/kmers-reader.C:143:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/bits.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/hexDump.C utility/kmers-writer.C: In destructor 'kmerCountFileWriter::~kmerCountFileWriter()': utility/kmers-writer.C:147:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 147 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from utility/kmers.H:29: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'kmerCountFileWriter::~kmerCountFileWriter()' at utility/kmers-writer.C:147:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/md5.C In file included from utility/bits.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/mt19937ar.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/objectStore.C In file included from utility/kmers.H:32, from utility/kmers-exact.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C: In member function 'bool kmerCountExactLookup::configure()': utility/kmers-exact.C:178:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 178 | fprintf(stderr, " p prefixes bits gigabytes (allowed: %lu GB)\n", _maxMemory >> 33); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:192:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 192 | fprintf(stderr, "%2u %14lu %16lu %9.3f (smallest)\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %14llu utility/kmers-exact.C:192:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 192 | fprintf(stderr, "%2u %14lu %16lu %9.3f (smallest)\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %16llu utility/kmers-exact.C:195:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 195 | fprintf(stderr, "%2u %14lu %16lu %9.3f (used)\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %14llu utility/kmers-exact.C:195:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 195 | fprintf(stderr, "%2u %14lu %16lu %9.3f (used)\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %16llu utility/kmers-exact.C:198:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 198 | fprintf(stderr, "%2u %14lu %16lu %9.3f\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %14llu utility/kmers-exact.C:198:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 198 | fprintf(stderr, "%2u %14lu %16lu %9.3f\n", pb, nprefix, space, bitsToGB(space)); | ~~~~^ ~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %16llu utility/kmers-exact.C:205:52: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 205 | fprintf(stderr, "Not enough memory to load %lu distinct %u-kmers.\n", _nSuffix, _Kbits / 2); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:210:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 210 | fprintf(stderr, "For %lu distinct %u-mers (with %u bits used for indexing and %u bits for tags):\n", _nSuffix, _Kbits / 2, _prefixBits, _suffixBits); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:212:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 212 | fprintf(stderr, " %7.3f GB memory for index (%lu elements %u bits wide)\n", bitsToGB(_nPrefix * _prePtrBits), _nPrefix, _prePtrBits); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:213:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 213 | fprintf(stderr, " %7.3f GB memory for tags (%lu elements %u bits wide)\n", bitsToGB(_nSuffix * _suffixBits), _nSuffix, _suffixBits); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:214:55: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 214 | fprintf(stderr, " %7.3f GB memory for data (%lu elements %u bits wide)\n", bitsToGB(_nSuffix * _valueBits), _nSuffix, _valueBits); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C: In member function 'void kmerCountExactLookup::allocate()': utility/kmers-exact.C:349:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 349 | fprintf(stderr, "Allocating space for %lu suffixes of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n", | ~~^ | | | long unsigned int | %llu 350 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin)); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C:349:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 349 | fprintf(stderr, "Allocating space for %lu suffixes of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n", | ~~^ | | | long unsigned int | %llu 350 | _nSuffix, _suffixBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin)); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C:361:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 361 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n", | ~~^ | | | long unsigned int | %llu 362 | _nSuffix, _valueBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin)); | ~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C:361:79: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 361 | fprintf(stderr, " %lu values of %u bits each -> %lu bits (%.3f GB) in blocks of %.3f MB\n", | ~~^ | | | long unsigned int | %llu 362 | _nSuffix, _valueBits, arraySize, bitsToGB(arraySize), bitsToMB(arrayBlockMin)); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C: In member function 'void kmerCountExactLookup::load()': utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 419 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 420 | _minValue, _maxValue, value, _valueBits); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C:419:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 419 | fprintf(stderr, "minValue " F_U32 " maxValue " F_U32 " value " F_U64 " bits " F_U32 "\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 420 | _minValue, _maxValue, value, _valueBits); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers-exact.C: In member function 'bool kmerCountExactLookup::exists_test(kmer)': utility/kmers-exact.C:508:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 508 | fprintf(stderr, "FAILED kmer 0x%016lx\n", kmer); | ~~~~~^ ~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers-exact.C:509:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 509 | fprintf(stderr, "FAILED prefix 0x%016lx\n", prefix); | ~~~~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers-exact.C:510:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 510 | fprintf(stderr, "FAILED suffix 0x%016lx\n", suffix); | ~~~~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utility/kmers-exact.C:512:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 512 | fprintf(stderr, "original %9lu %9lu\n", _suffixBgn[prefix], _suffixBgn[prefix + 1]); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %9llu utility/kmers-exact.C:512:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 512 | fprintf(stderr, "original %9lu %9lu\n", _suffixBgn[prefix], _suffixBgn[prefix + 1]); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %9llu utility/kmers-exact.C:513:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 513 | fprintf(stderr, "final %9lu %9lu\n", bgn, end); | ~~~^ ~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %9llu utility/kmers-exact.C:513:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 513 | fprintf(stderr, "final %9lu %9lu\n", bgn, end); | ~~~^ ~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %9llu utility/kmers-exact.C:524:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 524 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:524:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 524 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:524:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 524 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:524:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 524 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:524:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 524 | fprintf(stderr, "TEST bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~^ ~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:539:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 539 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:539:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 539 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:539:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 539 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %8llu utility/kmers-exact.C:539:59: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 539 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers-exact.C:539:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 539 | fprintf(stderr, "ITER bgn %8lu %8lu %8lu end -- dat %lu =?= %lu suffix\n", bgn, mid, end, tag, suffix); | ~~^ ~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/objectStore.C: In function 'bool fetchFromObjectStore(char*)': utility/objectStore.C:257:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 257 | args[1] = "download"; | ^~~~~~~~~~ utility/objectStore.C:258:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 258 | args[2] = "--overwrite"; | ^~~~~~~~~~~~~ utility/objectStore.C:259:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 259 | args[3] = "--no-progress"; | ^~~~~~~~~~~~~~~ utility/objectStore.C:260:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 260 | args[4] = "--output"; | ^~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/speedCounter.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/sweatShop.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, from correction/falconConsensus.C:73: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/falconConsensus.H:75, from correction/falconConsensus-alignTag.C:73: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from stores/sqCache.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C stores/sqCache.C: In constructor 'sqCache::sqCache(sqStore*, sqRead_which, uint64)': stores/sqCache.C:108:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 108 | fprintf(stderr, "sqCache: found %u %s reads with %lu bases.\n", nReads, toString(_which), nBases); | ~~^ ~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/sqCache.C: In member function 'void sqCache::sqCache_loadReads(uint32, uint32, bool)': stores/sqCache.C:356:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 356 | fprintf(stderr, "Loading %u reads and %lu bases from range %u-%u inclusive.\n", | ~~^ | | | long unsigned int | %llu 357 | nReads, nBases, bgnID, endID); | ~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C stores/sqReadDataWriter.C: In member function 'void sqReadDataWriter::sqReadDataWriter_writeBlob(writeBuffer*)': stores/sqReadDataWriter.C:109:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 109 | buffer->writeIFFchunk("BLOB"); | ^~~~~~ stores/sqReadDataWriter.C:110:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 110 | buffer->writeIFFchunk("NAME", _name, _nameLen); | ^~~~~~ stores/sqReadDataWriter.C:115:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 115 | buffer->writeIFFchunk("2SQR", rseq, rseq2Len); // Two-bit encoded sequence (ACGT only) | ^~~~~~ stores/sqReadDataWriter.C:117:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 117 | buffer->writeIFFchunk("3SQR", rseq, rseq3Len); // Three-bit encoded sequence (ACGTN) | ^~~~~~ stores/sqReadDataWriter.C:119:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 119 | buffer->writeIFFchunk("USQR", rseq, rseqULen); // Unencoded sequence | ^~~~~~ stores/sqReadDataWriter.C:124:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 124 | buffer->writeIFFchunk("2SQC", cseq, cseq2Len); // Two-bit encoded sequence (ACGT only) | ^~~~~~ stores/sqReadDataWriter.C:126:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 126 | buffer->writeIFFchunk("3SQC", cseq, cseq3Len); // Three-bit encoded sequence (ACGTN) | ^~~~~~ stores/sqReadDataWriter.C:128:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 128 | buffer->writeIFFchunk("USQC", cseq, cseqULen); // Unencoded sequence | ^~~~~~ stores/sqReadDataWriter.C:132:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 132 | buffer->closeIFFchunk("BLOB"); | ^~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C In file included from stores/sqStoreBlob.C:26: In function 'void makeBlobName(char*, uint32, char*)', inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/sqStore.H:37: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, inlined from 'sqStoreBlobWriter::sqStoreBlobWriter(const char*, sqStoreInfo*)' at stores/sqStoreBlob.C:46:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'void makeBlobName(char*, uint32, char*)', inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:73:17: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C In function 'void makeBlobName(char*, uint32, char*)', inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: stores/sqStore.H:126:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 126 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); stores/sqStore.H:126:36: note: directive argument in the range [0, 65535] In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void makeBlobName(char*, uint32, char*)' at stores/sqStore.H:126:11, inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:119:17: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovOverlap.C:217:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] 217 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C stores/ovStoreWriter.C:71:2: warning: #warning not failing if a valid store [-Wcpp] 71 | #warning not failing if a valid store | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 75 | dat.ovl.ahg5, dat.ovl.ahg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 75 | dat.ovl.ahg5, dat.ovl.ahg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 76 | dat.ovl.bhg5, dat.ovl.bhg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:71:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] 71 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 76 | dat.ovl.bhg5, dat.ovl.bhg3, | ~~~~~~~~~~~~ | | | int stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::checkInfo()': stores/sqStoreInfo.C:82:31: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] 82 | failed += fprintf(stderr, "ERROR: sqVersion in store = 0x%016" F_X64P ", differs from executable = 0x%016" F_X64P "\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/sqStoreInfo.C: In member function 'bool sqStoreInfo::readInfo8(char*)': stores/sqStoreInfo.C:229:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 229 | fprintf(stderr, "sqStore_loadInfo()-- Error: Unsupported historical version %lu detected.\n", _sqVersion); | ~~^ ~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu stores/sqStoreInfo.C: In member function 'void sqStoreInfo::writeInfo(char*)': stores/sqStoreInfo.C:333:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 333 | B->writeIFFobject("MAGC", _sqMagic); | ^~~~~~ stores/sqStoreInfo.C:334:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 334 | B->writeIFFobject("VERS", _sqVersion); | ^~~~~~ stores/sqStoreInfo.C:336:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 336 | B->writeIFFobject("LSIZ", _sqLibrarySize); | ^~~~~~ stores/sqStoreInfo.C:337:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 337 | B->writeIFFobject("RSIZ", _sqReadSize); | ^~~~~~ stores/sqStoreInfo.C:338:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 338 | B->writeIFFobject("MLB ", _sqMaxLibrariesBits); | ^~~~~~ stores/sqStoreInfo.C:339:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 339 | B->writeIFFobject("LNS ", _sqLibraryNameSize); | ^~~~~~ stores/sqStoreInfo.C:340:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 340 | B->writeIFFobject("MRB ", _sqMaxReadBits); | ^~~~~~ stores/sqStoreInfo.C:341:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 341 | B->writeIFFobject("MRLB", _sqMaxReadLenBits); | ^~~~~~ stores/sqStoreInfo.C:343:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 343 | B->writeIFFobject("NLIB", _numLibraries); | ^~~~~~ stores/sqStoreInfo.C:344:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 344 | B->writeIFFobject("NREA", _numReads); | ^~~~~~ stores/sqStoreInfo.C:345:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 345 | B->writeIFFobject("NBLO", _numBlobs); | ^~~~~~ stores/sqStoreInfo.C:347:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 347 | B->writeIFFarray("READ", _reads, sqRead_largest); | ^~~~~~ stores/sqStoreInfo.C:348:20: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 348 | B->writeIFFarray("BASE", _bases, sqRead_largest); | ^~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:204:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 204 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/sqStore.H:37, from stores/sqStoreConstructor.C:39: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:204:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 13 and 4109 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:212:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 212 | snprintf(No, FILENAME_MAX, "%s/libraries", _storePath); | ^~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:212:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:213:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 213 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:213:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 23 and 4126 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:216:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 216 | snprintf(No, FILENAME_MAX, "%s/reads", _storePath); | ^~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:216:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:217:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 217 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:217:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 19 and 4122 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:220:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 220 | snprintf(No, FILENAME_MAX, "%s/reads-rawu", _storePath); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:220:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:221:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 221 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawu", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:221:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:224:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 224 | snprintf(No, FILENAME_MAX, "%s/reads-rawc", _storePath); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:224:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:225:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 225 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawc", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:225:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:228:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 228 | snprintf(No, FILENAME_MAX, "%s/reads-coru", _storePath); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:228:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:229:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 229 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-coru", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:229:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:232:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 232 | snprintf(No, FILENAME_MAX, "%s/reads-corc", _storePath); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:232:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:233:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 233 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-corc", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:233:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 24 and 4127 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:236:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 236 | snprintf(No, FILENAME_MAX, "%s/info", _storePath); | ^~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:236:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:237:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 237 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:237:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 18 and 4121 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:240:35: warning: '/info.txt' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 240 | snprintf(No, FILENAME_MAX, "%s/info.txt", _storePath); | ^~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:240:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 10 and 4106 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:241:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 241 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info.txt", _storePath, V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:241:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 22 and 4125 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:207:34: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 207 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, _storePath, V); In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'sqStore::~sqStore()' at stores/sqStoreConstructor.C:207:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 13 and 4116 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:289:35: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 289 | snprintf(path, FILENAME_MAX, "%s/info", _storePath); AS_UTL_unlink(path); | ^~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:289:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:290:35: warning: '/libraries' directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 290 | snprintf(path, FILENAME_MAX, "%s/libraries", _storePath); AS_UTL_unlink(path); | ^~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:290:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 11 and 4107 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:291:35: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 291 | snprintf(path, FILENAME_MAX, "%s/reads", _storePath); AS_UTL_unlink(path); | ^~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:291:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:292:35: warning: '/reads-rawu' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 292 | snprintf(path, FILENAME_MAX, "%s/reads-rawu", _storePath); AS_UTL_unlink(path); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:292:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:293:35: warning: '/reads-rawc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 293 | snprintf(path, FILENAME_MAX, "%s/reads-rawc", _storePath); AS_UTL_unlink(path); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:293:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:294:35: warning: '/reads-coru' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 294 | snprintf(path, FILENAME_MAX, "%s/reads-coru", _storePath); AS_UTL_unlink(path); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:294:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:295:35: warning: '/reads-corc' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 295 | snprintf(path, FILENAME_MAX, "%s/reads-corc", _storePath); AS_UTL_unlink(path); | ^~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:295:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In member function 'void sqStore::sqStore_delete()': stores/sqStoreConstructor.C:296:35: warning: '/blobs' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 296 | snprintf(path, FILENAME_MAX, "%s/blobs", _storePath); AS_UTL_unlink(path); | ^~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void sqStore::sqStore_delete()' at stores/sqStoreConstructor.C:296:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': stores/ovStoreWriter.C:228:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); | ^~~~~~~ stores/ovStoreWriter.C:228:34: note: directive argument in the range [0, 536870910] 228 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/ovStore.H:37, from stores/ovStoreWriter.C:56: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:228:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 22 and 4129 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': stores/ovStoreWriter.C:237:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); | ^~~~~~~ stores/ovStoreWriter.C:237:34: note: directive argument in the range [0, 536870910] 237 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:237:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 23 and 4124 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': stores/ovStoreWriter.C:260:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 260 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)' at stores/ovStoreWriter.C:260:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.C: In member function 'void ovStore::testStore(bool)': stores/ovStore.C:182:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 182 | fprintf(stderr, "Success! Found %u reads with %lu overlaps out of %u reads total.\n", | ~~^ | | | long unsigned int | %llu 183 | nrds, novl, lid); | ~~~~ | | | uint64 {aka long long unsigned int} stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': stores/ovStoreWriter.C:344:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 344 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)' at stores/ovStoreWriter.C:344:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.C: In member function 'void ovStore::dumpMetaData(uint32, uint32)': stores/ovStore.C:493:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 493 | fprintf(stdout, "%9u %5u %5u %9u %9u %9lu\n", ii, | ~~~^ | | | long unsigned int | %9llu ...... 498 | _index[ii]._overlapID); | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': stores/ovStoreWriter.C:404:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 404 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::mergeInfoFiles()' at stores/ovStoreWriter.C:404:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': stores/ovStoreWriter.C:486:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 486 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeOverlapSlice()' at stores/ovStoreWriter.C:486:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': stores/ovStoreWriter.C:505:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 505 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::checkSortingIsComplete()' at stores/ovStoreWriter.C:505:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': stores/ovStoreWriter.C:506:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 506 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::checkSortingIsComplete()' at stores/ovStoreWriter.C:506:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.C: In constructor 'ovStore::ovStore(const char*, sqStore*)': stores/ovStore.C:109:35: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 109 | snprintf(name, FILENAME_MAX, "%s/evalues", _storePath); | ^~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/ovStore.H:37, from stores/ovStore.C:59: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'ovStore::ovStore(const char*, sqStore*)' at stores/ovStore.C:109:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:537:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 537 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeAllIntermediateFiles()' at stores/ovStoreWriter.C:537:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:540:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 540 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss); | ^ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeAllIntermediateFiles()' at stores/ovStoreWriter.C:540:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:557:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 557 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeAllIntermediateFiles()' at stores/ovStoreWriter.C:557:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:561:39: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 561 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeAllIntermediateFiles()' at stores/ovStoreWriter.C:561:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:565:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 565 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStoreSliceWriter::removeAllIntermediateFiles()' at stores/ovStoreWriter.C:565:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'int' [-Wformat=] 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'int' [-Wformat=] 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:359:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] 359 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 361 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc In file included from stores/ovStore.H:43, from stores/ovStoreFile.C:47: stores/ovStoreFile.H: In member function 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)': stores/ovStoreFile.H:89:40: warning: '.oc' directive output may be truncated writing 3 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 89 | snprintf(_name, FILENAME_MAX, "%s.oc", prefix); | ^~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/ovStore.H:37: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'ovFileOCW::ovFileOCW(sqStore*, const char*)' at stores/ovStoreFile.H:89:15, inlined from 'void ovFile::construct(sqStore*, const char*, ovFileType, uint32)' at stores/ovStoreFile.C:221:47: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 4 and 4100 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgTigSizeAnalysis.H:41, from stores/tgTigSizeAnalysis.C:42: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStore.C:44: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); | ^~~~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); | ^~~~~~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 143 | printSummary(out, "lenUnassembled", lenUnassembled); | ^~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 144 | printSummary(out, "lenBubble", lenBubble); | ^~~~~~~~~~~ stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 145 | printSummary(out, "lenContig", lenContig); | ^~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc In file included from stores/tgTig.H:36, from stores/tgTig.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgTigMultiAlignDisplay.C:42: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:191:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:191:33: note: using the range [-2147483648, 2147483647] for directive argument 191 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/tgStore.C:42: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::purgeVersion(uint32)' at stores/tgStore.C:191:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:192:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:192:33: note: using the range [-2147483648, 2147483647] for directive argument 192 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::purgeVersion(uint32)' at stores/tgStore.C:192:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::purgeVersion(uint32)': stores/tgStore.C:193:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:193:33: note: using the range [-2147483648, 2147483647] for directive argument 193 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::purgeVersion(uint32)' at stores/tgStore.C:193:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:594:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:594:33: note: using the range [-2147483648, 2147483647] for directive argument 594 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)' at stores/tgStore.C:594:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C stores/tgTig.C: In member function 'void tgTig::dumpLayout(FILE*, bool)': stores/tgTig.C:547:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 547 | fprintf(stderr, "ERROR: _bases length %ld\n", strlen(_bases)); | ~~^ ~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:626:40: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); | ^~~~~~~~ stores/tgStore.C:626:37: note: directive argument in the range [1, 2147483647] 626 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)' at stores/tgStore.C:626:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4119 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:637:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:637:33: note: using the range [-2147483648, 2147483647] for directive argument 637 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)' at stores/tgStore.C:637:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)': stores/tgStore.C:641:38: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:641:35: note: using the range [-2147483648, 2147483647] for directive argument 641 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)' at stores/tgStore.C:641:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgTig.C: In member function 'void tgTig::dumpFASTA(FILE*)': stores/tgTig.C:806:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 806 | ">tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgTig.C: In member function 'void tgTig::dumpFASTQ(FILE*)': stores/tgTig.C:826:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 826 | "@tig%08u len=" F_U32 " reads=" F_U32 " class=%s suggestRepeat=%s suggestBubble=%s suggestCircular=%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': stores/tgStore.C:695:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); | ^~~~~~~~ stores/tgStore.C:695:33: note: using the range [-2147483648, 2147483647] for directive argument 695 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); | ^~~~~~~~~~~~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'FILE* tgStore::openDB(uint32)' at stores/tgStore.C:695:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': stores/tgTig.C:565:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 565 | fgets(LINE, LINEmax, F); LINEnum++; | ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgTig.C:690:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 690 | fgets(LINE, LINEmax, F); LINEnum++; | ~~~~~^~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, from overlapInCore/overlapReadCache.C:30: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/liboverlap/prefixEditDistance-extend.C:69: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C In file included from utgcns/libNDalign/NDalign.C:36: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::processHits()': utgcns/libNDalign/NDalign.C:660:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 660 | display("NDalign::processHits()-- ", false); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/libNDalign/NDalign.C: In member function 'bool NDalign::scanDeltaForBadness(bool, bool)': utgcns/libNDalign/NDalign.C:724:15: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 724 | display("NDalign::scanForDeltaBadness()-- ", true); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignForward(bool, bool)': utgcns/libNDalign/NDalign.C:774:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 774 | display("NDalign::realignForward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/libNDalign/NDalign.C: In member function 'void NDalign::realignBackward(bool, bool)': utgcns/libNDalign/NDalign.C:838:13: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 838 | display("NDalign::realignBackward()-- ", displayAlign); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/dumpBlob.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBuild.C stores/ovStoreBuild.C: In function 'int main(int, char**)': stores/ovStoreBuild.C:125:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 125 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBuild.C:128:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 128 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gfa/gfa.C: In member function 'void gfaSequence::load(char*)': gfa/gfa.C:123:28: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 123 | findGFAtokenI(_features, "LN:i:", _length); | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreConfig.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreBucketizer.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreSorter.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreIndexer.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreDump.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/ovStoreStats.C stores/ovStoreConfig.C: In member function 'void ovStoreConfig::assignReadsToSlices(sqStore*, uint64, uint64)': stores/ovStoreConfig.C:288:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 288 | fprintf(stderr, "ERROR: expected %u slices, generated %u instead. %lu overlaps per slice allowed.\n", | ~~^ | | | long unsigned int | %llu 289 | _numSlices, slice, olapsPerSlice); | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} stores/ovStoreConfig.C: In function 'int main(int, char**)': stores/ovStoreConfig.C:372:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 372 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:375:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 375 | err.push_back("ERROR: No input overlap files (-L or last on the command line) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:378:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 378 | err.push_back("ERROR: Can't both -create -describe a config.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:381:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 381 | err.push_back("ERROR: Must supply one of -create or -describe.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreConfig.C:385:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 385 | err.push_back("ERROR: Memory (-M) must be at least 0.25 GB to account for overhead.\n"); // , OVSTORE_MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBucketizer.C: In function 'int main(int, char**)': stores/ovStoreBucketizer.C:139:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 139 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBucketizer.C:142:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 142 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBucketizer.C:145:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 145 | err.push_back("ERROR: No store configuration (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreBucketizer.C:148:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 148 | err.push_back("ERROR: Invalid or no bucket (-b) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreIndexer.C: In function 'int main(int, char**)': stores/ovStoreIndexer.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 80 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreIndexer.C:83:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 83 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreIndexer.C:86:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 86 | err.push_back("ERROR: No config (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreSorter.C: In function 'int main(int, char**)': stores/ovStoreSorter.C:167:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 167 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreSorter.C:170:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 170 | err.push_back("ERROR: no slice number (-F) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/sqStoreCreate.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/ovStoreDump.C:56: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C stores/ovStoreDump.C: In function 'int main(int, char**)': stores/ovStoreDump.C:832:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 832 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:835:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 835 | err.push_back("ERROR: no input ovlStore (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/ovStoreDump.C:838:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 838 | err.push_back("ERROR: -prefix is necessary for -binary output.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/ovStoreStats.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence stores/sqStoreDumpMetaData.C stores/sqStoreDumpFASTQ.C: In function 'int main(int, char**)': stores/sqStoreDumpFASTQ.C:459:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 459 | AS_UTL_writeFastQ(out[outid]->getFASTQ(), seq, seqLen, qlt, seqLen, "@%s\n", readName); | ^~~~~~~ stores/sqStoreDumpFASTQ.C:461:75: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 461 | AS_UTL_writeFastA(out[outid]->getFASTA(), seq, seqLen, 0, ">%s\n", readName); | ^~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:137:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 137 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); | ^~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/sqStoreDumpFASTQ.C:39: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'FILE* libOutput::openFASTQ()' at stores/sqStoreDumpFASTQ.C:137:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:135:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] 135 | snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s); | ^~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'FILE* libOutput::openFASTQ()' at stores/sqStoreDumpFASTQ.C:135:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()': stores/sqStoreDumpFASTQ.C:167:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 167 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s); | ^~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'FILE* libOutput::openFASTA()' at stores/sqStoreDumpFASTQ.C:167:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 8197 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()': stores/sqStoreDumpFASTQ.C:165:37: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] 165 | snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s); | ^~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'FILE* libOutput::openFASTA()' at stores/sqStoreDumpFASTQ.C:165:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 8 and 12293 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpMetaData.C: In function 'void dumpReads(sqStore*, uint32, uint32, sqRead_which)': stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 231 | seqs->sqStore_getReadSegm(rid), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} stores/sqStoreDumpMetaData.C:226:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 226 | fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 232 | seqs->sqStore_getReadByte(rid)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} stores/sqStoreDumpMetaData.C: In function 'void dumpHistogram(sqStore*, uint32, uint32, sqRead_which, bool)': stores/sqStoreDumpMetaData.C:277:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 277 | fprintf(stdout, "%lu\n", lengths[ii]); | ~~^ | | | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sqStoreDumpMetaData/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Isequence sequence/sequence-summarize.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreCompress.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); | ~~^ | | | long unsigned int | %llu sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); | ~~^ ~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 120 | fprintf(stdout, "%lu\n", lengths[ii]); | ~~^ | | | long unsigned int | %llu sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreDump.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreCompress.C:45: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/tgStoreDump.C:675:2: warning: #warning replace this with genericStatistics [-Wcpp] 675 | #warning replace this with genericStatistics | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigSizeAnalysis.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreLoad.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgStoreFilter.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/tgTigDisplay.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreDump.C:55: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/tgStoreDump.C: In function 'int main(int, char**)': stores/tgStoreDump.C:1166:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1166 | err.push_back("No sequence store (-S option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreDump.C:1169:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1169 | err.push_back("No tig store (-T option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreDump.C:1172:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1172 | err.push_back("No tig store version (-T option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreDump.C:1175:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1175 | err.push_back("-coverage needs and output prefix (-o option).\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreDump.C:1178:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 1178 | err.push_back("No DUMP TYPE supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadCorrectedReads.C In file included from stores/tgTig.H:36, from stores/tgTigSizeAnalysis.H:41, from stores/tgTigSizeAnalysis.C:42: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreLoad.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/tgTigSizeAnalysis.C: In member function 'void tgTigSizeAnalysis::printSummary(FILE*)': stores/tgTigSizeAnalysis.C:140:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 140 | printSummary(out, "lenSuggestRepeat", lenSuggestRepeat); | ^~~~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:141:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 141 | printSummary(out, "lenSuggestCircular", lenSuggestCircular); | ^~~~~~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:143:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 143 | printSummary(out, "lenUnassembled", lenUnassembled); | ^~~~~~~~~~~~~~~~ stores/tgTigSizeAnalysis.C:144:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 144 | printSummary(out, "lenBubble", lenBubble); | ^~~~~~~~~~~ stores/tgTigSizeAnalysis.C:145:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 145 | printSummary(out, "lenContig", lenContig); | ^~~~~~~~~~~ stores/tgStoreLoad.C: In function 'int main(int, char**)': stores/tgStoreLoad.C:194:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 194 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreLoad.C:196:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 196 | err.push_back("ERROR: no tig store (-T) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/tgStoreLoad.C:198:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 198 | err.push_back("ERROR: no input tig files supplied on command line or via -L option.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgTigDisplay.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/tgStoreFilter.C:45: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/loadCorrectedReads.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu stores/loadCorrectedReads.C: In function 'int main(int, char**)': stores/loadCorrectedReads.C:76:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 76 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadCorrectedReads.C:78:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 78 | err.push_back("ERROR: no tig store (-T) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadCorrectedReads.C:80:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 80 | err.push_back("ERROR: no input tigs supplied on command line and no -L file supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadCorrectedReads.C:185:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 185 | fprintf(stderr, "%9" F_U64P " %9" F_U64P " %35" F_U64P "\n", nLoadTot, nSkipTot, corInputs.size()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility stores/loadErates.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C meryl/meryl.C:261:2: warning: #warning HARD CODED NUMBER OF FILES! [-Wcpp] 261 | #warning HARD CODED NUMBER OF FILES! | ^~~~~~~ stores/loadTrimmedReads.C: In function 'int main(int, char**)': stores/loadTrimmedReads.C:180:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 180 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadErates.C: In function 'int main(int, char**)': stores/loadErates.C:214:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 214 | err.push_back("ERROR: No overlap store (-O) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadErates.C:217:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 217 | err.push_back("ERROR: No sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stores/loadErates.C:220:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 220 | err.push_back("ERROR: No input erate files (-L or last on the command line) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylInput.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/meryl.C:46: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylCountArray.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-count.C meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': stores/loadErates.C:86:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 86 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from stores/loadErates.C:43: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStore::addEvalues(std::vector&)' at stores/loadErates.C:86:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 17 and 4113 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': stores/loadErates.C:87:41: warning: '/evalues' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 87 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); | ^~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void ovStore::addEvalues(std::vector&)' at stores/loadErates.C:87:11: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4105 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylInput.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, from meryl/meryl.H:49: meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' meryl/merylCountArray.C:396:16: required from here utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' meryl/merylCountArray.C:397:16: required from here utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:331:42: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 331 | snprintf(indexName, FILENAME_MAX, "%s/merylIndex", optString); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from meryl/meryl.H:49: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at meryl/meryl.C:331:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:332:42: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 332 | snprintf(sqInfName, FILENAME_MAX, "%s/info", optString); | ^~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at meryl/meryl.C:332:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:333:42: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 333 | snprintf(sqRdsName, FILENAME_MAX, "%s/reads", optString); | ^~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at meryl/meryl.C:333:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ meryl/meryl.C: In function 'int main(int, char**)': meryl/meryl.C:594:54: warning: '%s' directive output may be truncated writing up to 4096 bytes into a region of size 996 [-Wformat-truncation=] 594 | snprintf(s, 1024, "Don't know what to do with '%s'.", optString); | ^~ ~~~~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'int main(int, char**)' at meryl/meryl.C:594:15: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 31 and 4127 bytes into a destination of size 1024 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp-count.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ meryl/merylOp-count.C: In function 'uint64 findMaxInputSizeForMemorySize(uint32, uint64)': meryl/merylOp-count.C:69:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 69 | fprintf(stderr, "For memory size %lu bytes\n", memSize); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu meryl/merylOp-count.C:112:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu 113 | wp, nKmers, | ~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu 113 | wp, nKmers, 114 | nPrefix, nSeg, | ~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:42: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu 113 | wp, nKmers, 114 | nPrefix, nSeg, | ~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu ...... 115 | mersPerSeg, | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:54: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu ...... 116 | basicMem, ptrMem, dataMem, | ~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:60: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %10llu ...... 116 | basicMem, ptrMem, dataMem, | ~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C:112:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 112 | fprintf(stderr, "%5u %10lu %10lu %10lu %10lu %10lu %10lu %12lu%s\n", | ~~~~^ | | | long unsigned int | %12llu ...... 116 | basicMem, ptrMem, dataMem, | ~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C: In function 'void findExpectedSimpleSize(uint64, uint64&)': meryl/merylOp-count.C:157:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 157 | fprintf(stderr, " -> %lu entries for counts up to %u.\n", nEntries, ((uint32)1 << lowBitsSize) - 1); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:158:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 158 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(lowMem), scaledUnit(lowMem)); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:160:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 160 | fprintf(stderr, " %lu input bases\n", nKmerEstimate); | ~~^ ~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:161:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:161:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 161 | fprintf(stderr, " -> expected max count of %lu, needing %lu extra bits.\n", expMaxCount, extraBits); | ~~^ ~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:163:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 163 | fprintf(stderr, " -> %lu %cbits memory used\n", scaledNumber(highMem), scaledUnit(highMem)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C:167:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 167 | fprintf(stderr, " %lu %cB memory needed\n", scaledNumber(totMem), scaledUnit(totMem)); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/merylOp-count.C: In member function 'void merylOperation::configureCounting(uint64, bool&, uint32&, uint64&, uint32&, uint64&)': meryl/merylOp-count.C:385:19: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 385 | fprintf(stderr, "Counting %lu (estimated)%s %s%s%s " F_U32 "-mers from " F_SIZE_T " input file%s:\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 386 | scaledNumber(_expNumKmers), scaledName(_expNumKmers), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-count.C: In member function 'void merylOperation::count(uint32, uint64, uint32, uint64)': meryl/merylOp-count.C:603:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 603 | fprintf(stderr, "Used %3.3f GB out of %3.3f GB to store %12lu kmers.\n", | ~~~~^ | | | long unsigned int | %12llu ...... 606 | kmersAdded); | ~~~~~~~~~~ | | | uint64 {aka long long unsigned int} In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp-countSimple.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ meryl/merylOp-countSimple.C: In member function 'void merylOperation::countSimple()': meryl/merylOp-countSimple.C:107:76: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 107 | fprintf(stderr, "Increasing to %u-bit storage (for kmer 0x%016lx).\n", | ~~~~~^ | | | long unsigned int | %016llx 108 | lowBitsSize + hib + 1, kidx); | ~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-countSimple.C:150:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 150 | fprintf(stderr, " nPrefix %lu\n", nPrefix); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu meryl/merylOp-countSimple.C:151:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 151 | fprintf(stderr, " nSuffix %lu\n", nSuffix); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu meryl/merylOp-countSimple.C:152:38: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 152 | fprintf(stderr, " sMask 0x%016lx\n", sMask); | ~~~~~^ ~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylOp.C meryl/merylOp-nextMer.C:98:2: warning: #warning "need to decide whic direction we're going?" [-Wcpp] 98 | #warning "need to decide whic direction we're going?" | ^~~~~~~ meryl/merylOp-nextMer.C:116:2: warning: #warning "rounding issues in word-frequency!" [-Wcpp] 116 | #warning "rounding issues in word-frequency!" | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/meryl-import.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-import.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/merylCountArray.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp-histogram.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp-nextMer.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ meryl/merylOp-nextMer.C: In member function 'void merylOperation::initializeThreshold()': meryl/merylOp-nextMer.C:113:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 113 | fprintf(stderr, "For fraction-distinct %f, found threshold %lu\n", _fracDist, _threshold); | ~~^ ~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu meryl/merylOp-nextMer.C:121:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 121 | fprintf(stderr, "For word-frequency %f, found threshold %lu\n", _wordFreq, _threshold); | ~~^ ~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu meryl/merylOp-nextMer.C: In member function 'bool merylOperation::nextMer()': meryl/merylOp-nextMer.C:612:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", | ~~^ | | | long unsigned int | %llu 613 | _kmer.toString(str), _actCount[0], _actCount[1]); | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylOp-nextMer.C:612:70: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 612 | fprintf(stdout, "kmer %s has value %lu in input 1 != value %lu in input 2\n", | ~~^ | | | long unsigned int | %llu 613 | _kmer.toString(str), _actCount[0], _actCount[1]); | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-lookup/meryl/meryl-lookup.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Imeryl -I/build/canu-2.0+dfsg/src -Iutility -Istores meryl/meryl-lookup.C In file included from utility/kmers.H:32, from meryl/meryl-import.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylOp.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} In file included from meryl/meryl.H:51, from meryl/merylCountArray.H:29, from meryl/meryl-import.C:31: meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ meryl/meryl-import.C: In function 'int main(int, char**)': meryl/meryl-import.C:92:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 92 | err.push_back("No input kmer file (-kmers) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-import.C:94:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 94 | err.push_back("No output database name (-output) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-import.C:96:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 96 | err.push_back("No kmer size (-k) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-import.C:233:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 233 | fprintf(stderr, "Found %lu kmers in the input.\n", nKmers); | ~~^ ~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence.C In file included from utility/kmers.H:32, from meryl/merylInput.H:30, from meryl/meryl.H:51, from meryl/merylCountArray.C:26: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/merylInput.H: In member function 'char* merylInput::inputType()': meryl/merylInput.H:51:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 51 | if (_operation) return("meryl-operation"); | ~^~~~~~~~~~~~~~~~~~ meryl/merylInput.H:52:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 52 | if (_stream) return("meryl-database"); | ~^~~~~~~~~~~~~~~~~ meryl/merylInput.H:53:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | if (_sequence) return("sequence-file"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:55:30: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | if (_store) return("canu-seqStore"); | ~^~~~~~~~~~~~~~~~ meryl/merylInput.H:58:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 58 | return("invalid-input"); | ~^~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-extract.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-extract.C In file included from utility/kmers.H:32, from meryl/meryl-lookup.C:28: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from /build/canu-2.0+dfsg/src/AS_global.H:89, from meryl/meryl.H:49: meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = unsigned int; uint64 = long long unsigned int]': meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = unsigned int; uint64 = long long unsigned int]' meryl/merylCountArray.C:396:16: required from here utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ meryl/merylCountArray.H: In instantiation of 'void swv::set(uint64, VALUE) [with VALUE = long long unsigned int; uint64 = long long unsigned int]': meryl/merylCountArray.C:205:23: required from 'swv* merylCountArray::unpackSuffixesAndValues(uint64) [with VALUE = long long unsigned int; uint64 = long long unsigned int]' meryl/merylCountArray.C:397:16: required from here utility/types.H:77:41: warning: right shift count >= width of type [-Wshift-count-overflow] 77 | #define uint64MASK(X) ((~uint64ZERO) >> (64 - (X))) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ meryl/merylCountArray.H:41:21: note: in expansion of macro 'uint64MASK' 41 | _s2 = suffix & uint64MASK(32); | ^~~~~~~~~~ utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-generate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-generate.C meryl/meryl-lookup.C: In function 'void dumpExistence(dnaSeqFile*, compressedFileWriter*, std::vector&, std::vector&)': meryl/meryl-lookup.C:83:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 83 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\n", | ~~^ | | | long unsigned int | %llu ...... 86 | kiter.position(), | ~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/meryl-lookup.C:97:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n", | ~~^ | | | long unsigned int | %llu ...... 100 | kiter.position(), | ~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} meryl/meryl-lookup.C:97:58: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n", | ~~^ | | | long unsigned int | %llu ...... 102 | kiter.fmer().toString(fString), fValue, | ~~~~~~ | | | uint64 {aka long long unsigned int} meryl/meryl-lookup.C:97:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 97 | fprintf(ofile->file(), "%s\t%u\t%lu\t%c\t%s\t%lu\t%s\t%lu\t%s\n", | ~~^ | | | long unsigned int | %llu ...... 103 | kiter.rmer().toString(rString), rValue, | ~~~~~~ | | | uint64 {aka long long unsigned int} meryl/meryl-lookup.C: In function 'void reportExistence(dnaSeqFile*, compressedFileWriter*, std::vector&, std::vector&)': meryl/meryl-lookup.C:134:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound); | ~~^ ~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/meryl-lookup.C:134:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/meryl-lookup.C:134:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(ofile->file(), "%s\t%lu\t%lu\t%lu\n", seq.name(), nKmer, klookup[0]->nKmers(), nKmerFound); | ~~^ ~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/meryl-lookup.C: In function 'void filter(dnaSeqFile*, dnaSeqFile*, compressedFileWriter*, compressedFileWriter*, std::vector&, bool)': meryl/meryl-lookup.C:204:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/meryl-lookup.C:204:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 204 | fprintf(stderr, "\nIncluding %lu reads (or read pairs) out of %lu.\n", nReadsFound, nReads); | ~~^ ~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu meryl/meryl-lookup.C: In function 'int main(int, char**)': meryl/meryl-lookup.C:285:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 285 | err.push_back("No input sequences (-sequence) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-lookup.C:287:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 287 | err.push_back("No query meryl database (-mers) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/meryl-lookup.C:289:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 289 | err.push_back("No report-type (-existence, etc) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-mutate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-mutate.C sequence/sequence.C: In function 'int main(int, char**)': sequence/sequence.C:414:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 414 | err.push_back("ERROR: No mode (summarize, extract, generate or simulate) specified.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/sequence.C:418:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 418 | err.push_back("ERROR: No input sequence files supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/sequence.C:422:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 422 | err.push_back("ERROR: No input sequence files supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/sequence.C:428:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 428 | err.push_back("ERROR: No reference genome sequence (-genome) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence/sequence.C:432:21: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 432 | err.push_back("ERROR: No input sequence files supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-sample.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-sample.C sequence/sequence-sample.C: In function 'void doSample_paired(std::vector&, sampleParameters&)': sequence/sequence-sample.C:272:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 272 | AS_UTL_writeFastA(outFile1, seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); | ^~~~~~~ sequence/sequence-sample.C:273:69: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 273 | AS_UTL_writeFastA(outFile2, seq2.bases(), seq2.length(), 0, ">%s\n", seq2.name()); | ^~~~~~~ sequence/sequence-sample.C: In function 'void doSample_single(std::vector&, sampleParameters&)': sequence/sequence-sample.C:417:73: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 417 | AS_UTL_writeFastA(outFiles[of], seq1.bases(), seq1.length(), 0, ">%s\n", seq1.name()); | ^~~~~~~ sequence/sequence-generate.C: In function 'void doGenerate(generateParameters&)': sequence/sequence-generate.C:92:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 92 | ">random%08 " F_U64P "\n", nSeqs); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister.C sequence/sequence-mutate.C: In function 'void doMutate(std::vector&, mutateParameters&)': sequence/sequence-mutate.C:160:50: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 160 | AS_UTL_writeFastA(stdout, nBases, oLen, 0, ">%s\n", seq.name()); | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-emit-fast.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-fast.C In file included from sequence/sequence-shiftregister.C:31: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-shiftregister-search-slow.C In file included from sequence/sequence-shiftregister-emit-fast.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-shiftregister-emit-fast.C: In function 'void emitShiftRegisterFast(shiftRegisterParameters&)': sequence/sequence-shiftregister-emit-fast.C:52:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 52 | fprintf(stderr, "Emitting %lu bases, plus an extra %u.\n", srPar.length - srPar.order - 1 - 1, srPar.order - 1); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-shiftregister-emit-fast.C:53:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 53 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr)); | ~~~~^ ~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-emit-fast.C:54:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 54 | fprintf(stderr, " cyclen %lu\n", cyclen); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-emit-fast.C:55:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 55 | fprintf(stderr, " cycmax %lu\n", cycmax); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-emit-fast.C:56:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 56 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv)); | ~~~~^ ~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-emit-fast.C:57:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 57 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax)); | ~~~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-emit-fast.C:58:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 58 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask)); | ~~~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-simulate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-simulate.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -DCANU -Isequence -I/build/canu-2.0+dfsg/src -Iutility sequence/sequence-summarize.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C In file included from sequence/sequence-shiftregister-search-fast.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-shiftregister-search-fast.C: In function 'void searchShiftRegisterFast(shiftRegisterParameters&)': sequence/sequence-shiftregister-search-fast.C:47:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 47 | fprintf(stderr, " sr %0*lo\n", srPar.order, expandTo3(sr)); | ~~~~^ ~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-search-fast.C:48:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 48 | fprintf(stderr, " cyclen %lu\n", cyclen); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-search-fast.C:49:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 49 | fprintf(stderr, " cycmax %lu\n", cycmax); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-search-fast.C:50:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 50 | fprintf(stderr, " sv %0*lo\n", srPar.order, expandTo3(sv)); | ~~~~^ ~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-search-fast.C:51:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 51 | fprintf(stderr, " svmax %0*lo\n", srPar.order, expandTo3(svmax)); | ~~~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-search-fast.C:52:33: warning: format '%lo' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 52 | fprintf(stderr, " svmask %0*lo\n", srPar.order, expandTo3(svmask)); | ~~~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %0*llo sequence/sequence-shiftregister-search-fast.C:131:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", | ~~~~^ | | | long unsigned int | %14llu 132 | cyclen, | ~~~~~~ | | | uint64 {aka long long unsigned int} sequence/sequence-shiftregister-search-fast.C:131:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", | ~~~~^ | | | long unsigned int | %14llu 132 | cyclen, 133 | cycmax, | ~~~~~~ | | | uint64 {aka long long unsigned int} sequence/sequence-shiftregister-search-fast.C:131:59: warning: format '%lo' expects argument of type 'long unsigned int', but argument 7 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 131 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %0*lo\n", | ~~~~^ | | | long unsigned int | %0*llo ...... 136 | expandTo3(sv)); | ~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} In file included from sequence/sequence-shiftregister-search-slow.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-shiftregister-search-slow.C: In function 'void searchShiftRegisterSlow(shiftRegisterParameters&)': sequence/sequence-shiftregister-search-slow.C:154:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 154 | fprintf(stderr, " cyclen %lu\n", cyclen); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-search-slow.C:155:31: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 155 | fprintf(stderr, " cycmax %lu\n", cycmax); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu sequence/sequence-shiftregister-search-slow.C:209:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", | ~~~~^ | | | long unsigned int | %14llu 210 | cyclen, | ~~~~~~ | | | uint64 {aka long long unsigned int} sequence/sequence-shiftregister-search-slow.C:209:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 209 | fprintf(stdout, "%14lu/%14lu %7.3f%% for vector %s\n", | ~~~~^ | | | long unsigned int | %14llu 210 | cyclen, 211 | cycmax, | ~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogramSimple(std::vector)': sequence/sequence-summarize.C:106:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); | ~~^ | | | long unsigned int | %llu sequence/sequence-summarize.C:106:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 106 | fprintf(stdout, "%lu\t%lu\n", lengths[bgn], end - bgn); | ~~^ ~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu sequence/sequence-summarize.C: In function 'void doSummarize_dumpLengths(std::vector)': sequence/sequence-summarize.C:120:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] 120 | fprintf(stdout, "%lu\n", lengths[ii]); | ~~^ | | | long unsigned int | %llu sequence/sequence-simulate.C: In member function 'void simulateParameters::finalize()': sequence/sequence-simulate.C:44:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 44 | char *path = findSharedFile("share/sequence", distribName); | ^~~~~~~~~~~~~~~~ sequence/sequence-summarize.C: In function 'void doSummarize_lengthHistogram(std::vector, uint64, bool)': sequence/sequence-summarize.C:290:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 290 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", 0.0, lengths.size(), lSum, histPlot[hp++]); // Occurs if only empty sequences in the input! | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} sequence/sequence-summarize.C:292:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 292 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " || %s\n", (double)lSum / genomeSize, lengths.size(), lSum, histPlot[hp++]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} sequence/sequence-summarize.C:294:21: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 294 | fprintf(stdout, "%07.3fx %9" F_U64P " %12" F_U64P " ||\n", (double)lSum / genomeSize, lengths.size(), lSum); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ | | | std::vector::size_type {aka unsigned int} sequence/sequence-simulate.C: In function 'void doSimulate_loadSequences(simulateParameters&, std::vector&, uint64&)': sequence/sequence-simulate.C:89:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 89 | fprintf(stderr, "Loaded %lu sequences.\n", seqs.size()); | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u sequence/sequence-simulate.C: In function 'void doSimulate_extract(simulateParameters&, std::vector&, uint64, mtRandom&, uint64, uint64)': sequence/sequence-simulate.C:194:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", | ~~^ | | | long unsigned int | %llu 195 | nReads+1, | ~~~~~~~~ | | | uint64 {aka long long unsigned int} sequence/sequence-simulate.C:194:48: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 194 | fprintf(stdout, ">read=%lu,%s,position=%lu,length=%u,%s\n", | ~~^ | | | long unsigned int | %llu ...... 197 | position, | ~~~~~~~~ | | | uint64 {aka long long unsigned int} In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore-Build_Hash_Index.C:67: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore.C:51: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': overlapInCore/overlapInCore-Build_Hash_Index.C:258:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | fgets(line, 1024, F); | ~~~~~^~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore-Find_Overlaps.C:71: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore-Output.C:67: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore-Process_Overlaps.C:71: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapInCore/overlapInCore.H:66, from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C overlapInCore/overlapPair.C:479:2: warning: #warning do we need to check for contained too? [-Wcpp] 479 | #warning do we need to check for contained too? | ^~~~~~~ overlapInCore/overlapInCorePartition.C: In function 'int main(int, char**)': overlapInCore/overlapInCorePartition.C:430:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 430 | FILE *BAT = openOutput(outputPrefix, "ovlbat"); | ^~~~~~~~ overlapInCore/overlapInCorePartition.C:431:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 431 | FILE *JOB = openOutput(outputPrefix, "ovljob"); | ^~~~~~~~ overlapInCore/overlapInCorePartition.C:432:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 432 | FILE *OPT = openOutput(outputPrefix, "ovlopt"); | ^~~~~~~~ overlapInCore/overlapInCorePartition.C:445:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 445 | renameToFinal(outputPrefix, "ovlbat"); | ^~~~~~~~ overlapInCore/overlapInCorePartition.C:446:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 446 | renameToFinal(outputPrefix, "ovljob"); | ^~~~~~~~ overlapInCore/overlapInCorePartition.C:447:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 447 | renameToFinal(outputPrefix, "ovlopt"); | ^~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Imhap/liboverlap mhap/mhapConvert.C overlapInCore/overlapImport.C: In function 'int main(int, char**)': overlapInCore/overlapImport.C:158:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 158 | err.push_back("ERROR: no input seqStore (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:161:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 161 | err.push_back("ERROR: no input overlap files supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 274 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iminimap/liboverlap minimap/mmapConvert.C overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': overlapInCore/edalign.C:38:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | fgets(line, lineMax, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from overlapInCore/overlapReadCache.H:37, from overlapInCore/overlapPair.C:44: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu overlapInCore/overlapPair.C: In function 'void* recomputeOverlaps(void*)': overlapInCore/overlapPair.C:429:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 429 | if (extendAlignment(bRead, bbgn, bend, blen, "B", bID, | ^~~ overlapInCore/overlapPair.C:430:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 430 | aRead, abgn, aend, alen, "A", aID, | ^~~ overlapInCore/overlapPair.C:437:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 437 | if (extendAlignment(aRead, abgn, aend, alen, "A", aID, | ^~~ overlapInCore/overlapPair.C:438:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 438 | bRead, bbgn, bend, blen, "B", bID, | ^~~ overlapInCore/overlapPair.C:506:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 506 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb5", bID, | ^~~~~ overlapInCore/overlapPair.C:507:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 507 | aRead, abgn, aend, alen, "Ab5", aID, | ^~~~~ overlapInCore/overlapPair.C:532:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 532 | if (extendAlignment(aRead, abgn, aend, alen, "Aa5", aID, | ^~~~~ overlapInCore/overlapPair.C:533:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 533 | bRead, bbgn, bend, blen, "Ba5", bID, | ^~~~~ overlapInCore/overlapPair.C:560:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 560 | if (extendAlignment(aRead, abgn, aend, alen, "Aa3", aID, | ^~~~~ overlapInCore/overlapPair.C:561:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 561 | bRead, bbgn, bend, blen, "Ba3", bID, | ^~~~~ overlapInCore/overlapPair.C:586:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 586 | if (extendAlignment(bRead, bbgn, bend, blen, "Bb3", bID, | ^~~~~ overlapInCore/overlapPair.C:587:56: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 587 | aRead, abgn, aend, alen, "Ab3", aID, | ^~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iwtdbg/liboverlap wtdbg/wtdbgConvert.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionOverlaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/generateCorrectionLayouts.C minimap/mmapConvert.C: In function 'int main(int, char**)': minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 7 has type 'int' [-Wformat=] 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 142 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 143 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:139:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] 139 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 143 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C mhap/mhapConvert.C: In function 'int main(int, char**)': mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'int' [-Wformat=] 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'int' [-Wformat=] 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 162 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'int' [-Wformat=] 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 163 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:158:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'int' [-Wformat=] 158 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 163 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores correction/filterCorrectionLayouts.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, from utgcns/stashContains.C:30: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from wtdbg/wtdbgConvert.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/generateCorrectionLayouts.C:37: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu correction/generateCorrectionLayouts.C: In function 'void generateLayout(tgTig*, uint16*, uint32, double, double, ovOverlap*, uint32, FILE*)': correction/generateCorrectionLayouts.C:118:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 118 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - low quality (threshold %.2f)\n", | ~~~^ | | | long unsigned int | %5llu 119 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), maxEvidenceErate); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} correction/generateCorrectionLayouts.C:125:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 125 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - too short (threshold %u)\n", | ~~~^ | | | long unsigned int | %5llu 126 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), minEvidenceLength); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} correction/generateCorrectionLayouts.C:133:26: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 133 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - filtered by global filter (threshold " F_U16 ")\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate(), olapThresh[ovl[oo].b_iid]); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} correction/generateCorrectionLayouts.C:140:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 140 | fprintf(logFile, " filter read %9u at position %6u,%6u length %5lu erate %.3f - duplicate\n", | ~~~^ | | | long unsigned int | %5llu 141 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate()); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} correction/generateCorrectionLayouts.C:146:73: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 146 | fprintf(logFile, " allow read %9u at position %6u,%6u length %5lu erate %.3f\n", | ~~~^ | | | long unsigned int | %5llu 147 | ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength, ovl[oo].erate()); | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns correction/falconsense.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns utgcns/stashContains.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from correction/filterCorrectionLayouts.C:29: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Iutgcns haplotyping/splitHaplotype.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from correction/falconsense.C:32: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, from utgcns/stashContains.C:30: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads.C In file included from utility/kmers.H:32, from haplotyping/splitHaplotype.C:34: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/kmers.H: In member function 'void kmerCountFileIndex::set(uint64, FILE*, uint64)': utility/kmers.H:594:42: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, | ~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:57: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~~~^ | | | long unsigned int | %016llx 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:62: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:67: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu 595 | prefix, 596 | _blockPrefix, _blockPosition, _numKmers, | ~~~~~~~~~ | | | uint64 {aka long long unsigned int} utility/kmers.H:594:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 594 | fprintf(stderr, "set prefix 0x%016lx from [0x%016lx %8lu %8lu] to [%8lu %8lu]\n", | ~~~^ | | | long unsigned int | %8llu ...... 597 | AS_UTL_ftell(F), _numKmers + nKmers); | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} correction/falconsense.C: In function 'void generateFalconConsensus(falconConsensus*, tgTig*, sqCache*, std::map&, bool, uint32)': correction/falconsense.C:207:41: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem); | ~~~~^ ~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %10llu correction/falconsense.C:207:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 207 | fprintf(stdout, "(%6u) memory act %10lu est %10lu act/est %.2f", len, fc->getRSS(), mem, fc->getRSS() * 100.0 / mem); | ~~~~^ ~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %10llu correction/falconsense.C: In function 'int main(int, char**)': correction/falconsense.C:359:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 359 | err.push_back("ERROR: no seqStore input (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ correction/falconsense.C:362:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 362 | err.push_back("ERROR: no corStore input (-C) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from correction/errorEstimate.C:34: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu haplotyping/splitHaplotype.C: In member function 'void hapData::initializeKmerTable(uint32)': haplotyping/splitHaplotype.C:443:34: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 443 | fprintf(stderr, "-- loaded %lu kmers.\n", nKmers); | ~~^ ~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu haplotyping/splitHaplotype.C: In function 'void outputReadBatch(void*, void*)': haplotyping/splitHaplotype.C:707:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 707 | ">%s\n", s->_names[ii].string()); | ^~~~~~~ haplotyping/splitHaplotype.C: In function 'int main(int, char**)': haplotyping/splitHaplotype.C:771:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 771 | err.push_back("No input sequences supplied with either (-S) or (-R).\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplotyping/splitHaplotype.C:773:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 773 | err.push_back("Only one type of input reads (-S or -R) supported.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplotyping/splitHaplotype.C:775:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 775 | err.push_back("Not enough haplotypes (-H) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplotyping/splitHaplotype.C:854:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 854 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_haps[ii]->nReads, G->_haps[ii]->nBases, G->_haps[ii]->outputName); | ~~~~^ | | | long unsigned int | %12llu haplotyping/splitHaplotype.C:855:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 855 | fprintf(stdout, "-- %8u reads %12lu bases written to haplotype file %s.\n", G->_ambiguousReads, G->_ambiguousBases, G->_ambiguousName); | ~~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %12llu haplotyping/splitHaplotype.C:857:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 857 | fprintf(stdout, "-- %8u reads %12lu bases filtered for being too short.\n", G->_filteredReads, G->_filteredBases); | ~~~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %12llu correction/falconsense.C: In function 'void loadReadList(char*, uint32, uint32, std::set&)': correction/falconsense.C:70:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | for (fgets(L, 1024, R); | ~~~~~^~~~~~~~~~~~ correction/falconsense.C:72:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(L, 1024, R)) { | ~~~~~^~~~~~~~~~~~ overlapBasedTrimming/trimReads.C: In function 'int main(int, char**)': overlapBasedTrimming/trimReads.C:480:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 480 | readsIn .generatePlots(outputPrefix, "inputReads", 250); | ^~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:481:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 481 | deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); | ^~~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:482:41: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 482 | noTrimIn .generatePlots(outputPrefix, "inputNoTrimReads", 250); | ^~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:492:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 492 | readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); | ^~~~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:493:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 493 | noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); | ^~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:494:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 494 | deletedOut .generatePlots(outputPrefix, "outputDeletedReads", 250); | ^~~~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:495:43: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 495 | noChangeOut.generatePlots(outputPrefix, "outputUnchangedReads", 250); | ^~~~~~~~~~~~~~~~~~~~~~ overlapBasedTrimming/trimReads.C:503:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 503 | trim5.generatePlots(outputPrefix, "trim5", 25); | ^~~~~~~ overlapBasedTrimming/trimReads.C:504:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 504 | trim3.generatePlots(outputPrefix, "trim3", 25); | ^~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-bestEdge.C In file included from overlapBasedTrimming/trimReads.C:31: overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(char*, char*, uint32)': overlapBasedTrimming/trimStat.H:74:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 74 | system(N); | ~~~~~~^~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/trimReads-largestCovered.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-workUnit.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-subReads.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/splitReads-trimBad.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustNormal.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/adjustFlipped.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores overlapBasedTrimming/mergeRanges.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C overlapBasedTrimming/mergeRanges.C: In function 'int main(int, char**)': overlapBasedTrimming/mergeRanges.C:77:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 77 | err.push_back("ERROR: no sequence store (-S) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapAlign/overlapAlign.C:39: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapAlign/computeOverlapAlignment.C:32: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu overlapAlign/computeOverlapAlignment.C: In member function 'void maComputation::computeOverlapAlignment(uint32, uint32, double, uint32, uint32)': overlapAlign/computeOverlapAlignment.C:581:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 581 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into | ^~~ overlapAlign/computeOverlapAlignment.C:582:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 582 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends. | ^~~ overlapAlign/computeOverlapAlignment.C:626:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 626 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into | ^~~ overlapAlign/computeOverlapAlignment.C:627:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 627 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. | ^~~ overlapAlign/computeOverlapAlignment.C:674:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 674 | if (computeAlignment(_bRead, bbgn, bend, blen, "B", _bID, // Align all of sequence B into | ^~~ overlapAlign/computeOverlapAlignment.C:675:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 675 | _aRead, abgn, aend, alen, "A", _aID, // sequence A with free ends. | ^~~ overlapAlign/computeOverlapAlignment.C:719:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 719 | if (computeAlignment(_aRead, abgn, aend, alen, "A", _aID, // Align all of sequence A into | ^~~ overlapAlign/computeOverlapAlignment.C:720:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 720 | _bRead, bbgn, bend, blen, "B", _bID, // sequence B with free ends. | ^~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapAlign/computeAlignments.C:36: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from stores/sqCache.H:30, from overlapAlign/trimRead.C:33: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C overlapErrorAdjustment/correctOverlaps-Correct_Frags.C: In function 'void Correct_Frags(coParameters*, sqStore*, FILE*)': overlapErrorAdjustment/correctOverlaps-Correct_Frags.C:281:74: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 281 | AS_UTL_writeFastA(correctedReads, read.bases, read.basesLen, 60, ">%d\n", curID); | ^~~~~~~ overlapErrorAdjustment/findErrors-Dump.C: In function 'int main(int, char**)': overlapErrorAdjustment/findErrors-Dump.C:66:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 66 | char *typeName[13] = { "IDENT", | ^~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:67:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 67 | "DELETE", | ^~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:68:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 68 | "A_SUBST", | ^~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:69:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 69 | "C_SUBST", | ^~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:70:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 70 | "G_SUBST", | ^~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:71:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 71 | "T_SUBST", | ^~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:72:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 72 | "A_INSERT", | ^~~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:73:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 73 | "C_INSERT", | ^~~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:74:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 74 | "G_INSERT", | ^~~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:75:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 75 | "T_INSERT", | ^~~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:76:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 76 | "NO_VOTE", | ^~~~~~~~~ overlapErrorAdjustment/findErrors-Dump.C:77:27: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 77 | "EXTENSION", | ^~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/bogart.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_AssemblyGraph.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_BestOverlapGraph.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ChunkGraph.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_AssemblyGraph.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_CreateUnitigs.C bogart/AS_BAT_CreateUnitigs.C:486:2: warning: #warning deviationGraph hard coded [-Wcpp] 486 | #warning deviationGraph hard coded | ^~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/bogart.C:46: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu bogart/bogart.C: In function 'int main(int, char**)': bogart/bogart.C:338:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 338 | if (erateGraph < 0.0) err.push_back("Invalid overlap error threshold (-eg option); must be at least 0.0.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogart/bogart.C:339:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 339 | if (erateMax < 0.0) err.push_back("Invalid overlap error threshold (-eM option); must be at least 0.0.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogart/bogart.C:340:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 340 | if (prefix == NULL) err.push_back("No output prefix name (-o option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogart/bogart.C:341:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 341 | if (seqStorePath == NULL) err.push_back("No sequence store (-S option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogart/bogart.C:342:46: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 342 | if (ovlStorePath == NULL) err.push_back("No overlap store (-O option) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_BestOverlapGraph.C:46: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu bogart/bogart.C:736:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 736 | writeTigsToStore(contigs, prefix, "ctg", true); | ^~~~~ bogart/bogart.C:756:37: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 756 | writeTigsToStore(unitigs, prefix, "utg", true); | ^~~~~ In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_CreateUnitigs.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DetectSpurs.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_DropDeadEnds.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Instrumentation.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_DetectSpurs.C:31: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Logging.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MarkRepeatReads.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_MergeOrphans.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_DropDeadEnds.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OptimizePositions.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Instrumentation.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_MarkRepeatReads.C:29: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu bogart/AS_BAT_Instrumentation.C: In function 'void reportTigs(TigVector&, const char*, const char*, uint64)': bogart/AS_BAT_Instrumentation.C:421:46: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 421 | writeTigsToStore(tigs, getLogFilePrefix(), "tig", false); | ^~~~~ bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': bogart/AS_BAT_Logging.C:91:37: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); | ^~~~ bogart/AS_BAT_Logging.C:91:34: note: using the range [-2147483648, 2147483647] for directive argument 91 | snprintf(path, FILENAME_MAX, "%s.num%03d.log", name, part); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from bogart/AS_BAT_Logging.H:41, from bogart/AS_BAT_Logging.C:38: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:91:13: /usr/include/i386-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 12 and 4115 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Outputs.C bogart/AS_BAT_MarkRepeatReads.C: In function 'uint32 splitTig(TigVector&, Unitig*, std::vector&, Unitig**, int32*, uint32*, uint32*, bool)': bogart/AS_BAT_MarkRepeatReads.C:170:64: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 170 | fprintf(stderr, "Failed to place read %u at %d-%d with %lu BPs:\n", frg.ident, frgbgn, frgend, BP.size()); | ~~^ ~~~~~~~~~ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_OverlapCache.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_OptimizePositions.C:44: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_MergeOrphans.C:35: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu bogart/AS_BAT_MergeOrphans.C: In function 'void findPotentialOrphans(TigVector&, BubTargetList&)': bogart/AS_BAT_MergeOrphans.C:196:69: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'int' [-Wformat=] 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", | ~~^ | | | long int | %d 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, | ~~~~~~~~~~~~~~ | | | int bogart/AS_BAT_MergeOrphans.C:196:73: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'int' [-Wformat=] 196 | fprintf(stderr, "read %u at %u %u olap to read %u hangs %ld %ld -> coords %d %d\n", | ~~^ | | | long int | %d 197 | ovl[oi].a_iid, rdA->position.bgn, rdA->position.end, 198 | ovl[oi].b_iid, ovl[oi].a_hang, ovl[oi].b_hang, | ~~~~~~~~~~~~~~ | | | int In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_OverlapCache.C:49: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Outputs.C:47: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from bogart/AS_BAT_Outputs.C:51: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceContains.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PopulateUnitig.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PlaceContains.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_PromoteToSingleton.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_ReadInfo.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PlaceReadUsingOverlaps.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PopulateUnitig.C:42: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_PromoteToSingleton.C:40: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SetParentAndHang.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_SplitDiscontinuous.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigGraph.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_TigVector.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SetParentAndHang.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_SplitDiscontinuous.C:41: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_AssemblyGraph.H:32, from bogart/AS_BAT_TigGraph.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_AddRead.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_TigVector.C:28: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig.C:39: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogus.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores bogus/bogusUtil.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig_AddRead.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/utgcns.C:46: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C In file included from bogart/AS_BAT_Unitig.H:49, from bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C:43: utility/stddev.H: In member function 'void histogramStatistics::finalizeData()': utility/stddev.H:451:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu utility/stddev.H:451:83: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 451 | fprintf(stderr, "finalizeData()-- Failed at ii=%lu for _histogramMax=%lu\n", ii, _histogramMax); | ~~^ ~~~~~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:452:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 452 | fprintf(stderr, "finalizeData()-- _median=%lu\n", _median); | ~~^ ~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utility/stddev.H:453:68: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 453 | fprintf(stderr, "finalizeData()-- deviation=%lu\n", deviation); | ~~^ ~~~~~~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utgcns/utgcns.C: In function 'uint32 createPartitions_greedilyPartition(cnsParameters&, tigInfo*, uint32)': utgcns/utgcns.C:294:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n", | ~~~^ | | | long unsigned int | %9llu 295 | tigs[ti].tigID, 296 | tigs[ti].tigChildren, | ~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C:294:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n", | ~~~^ | | | long unsigned int | %9llu ...... 297 | tigs[ti].tigLength, | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C:294:46: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 294 | fprintf(stderr, "%9u %9lu %9lu %12lu %9.3f %9u\n", | ~~~~^ | | | long unsigned int | %12llu ...... 298 | tigs[ti].consensusArea, | ~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C: In function 'uint64* createPartitions_outputPartitions(cnsParameters&, tigInfo*, uint32, uint32)': utgcns/utgcns.C:363:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 363 | parts[pi]->writeIFFobject("MAGC", magc); | ^~~~~~ utgcns/utgcns.C:364:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 364 | parts[pi]->writeIFFobject("VERS", vers); | ^~~~~~ utgcns/utgcns.C:365:31: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 365 | parts[pi]->writeIFFobject("DEFV", defv); | ^~~~~~ utgcns/utgcns.C: In function 'void createPartitions(cnsParameters&)': utgcns/utgcns.C:419:33: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n", | ~~~^ | | | long unsigned int | %9llu 420 | tigs[ti].tigID, 421 | tigs[ti].tigChildren, | ~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C:419:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n", | ~~~^ | | | long unsigned int | %9llu ...... 422 | tigs[ti].tigLength, | ~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C:419:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 419 | fprintf(partFile, "%9u %9lu %9lu %12lu %9.3f %9u %9.3f\n", | ~~~~^ | | | long unsigned int | %12llu ...... 423 | tigs[ti].consensusArea, | ~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long long unsigned int} utgcns/utgcns.C: In function 'std::map* loadPartitionedReads(char*)': utgcns/utgcns.C:582:75: warning: format '%lx' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 582 | fprintf(stderr, "File '%s' isn't a utgcns seqFile: found magic 0x%016lx.\n", seqFile, magc), exit(1); | ~~~~~^ ~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %016llx utgcns/utgcns.C:588:82: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 588 | fprintf(stderr, "File '%s' is a utgcns seqFile, but an unsupported version %lu.\n", seqFile, vers), exit(1); | ~~^ ~~~~ | | | | | uint64 {aka long long unsigned int} | long unsigned int | %llu utgcns/utgcns.C: In function 'int main(int, char**)': utgcns/utgcns.C:887:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 887 | err.push_back("ERROR: No sequence data! Need one of seqStore (-S), read file (-R) or package (-p).\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utgcns/utgcns.C:890:19: warning: ISO C++ forbids converting a string constant to 'std::vector::value_type' {aka 'char*'} [-Wwrite-strings] 890 | err.push_back("ERROR: No tigStore (-T) OR no test tig (-t) OR no package (-p) supplied.\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/stashContains.H:35, from utgcns/stashContains.C:30: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu bogus/bogusUtil.C: In function 'void loadNucmer(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:125:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets(inLine, 1024, inFile); // (file paths) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:126:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 126 | fgets(inLine, 1024, inFile); // NUCMER | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:127:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | fgets(inLine, 1024, inFile); // (blank) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:128:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 128 | fgets(inLine, 1024, inFile); // (header) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:142:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 142 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:200:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C: In function 'void loadSnapper(char*, std::vector&, std::map, int>&, std::vector >&, std::vector&, std::map, unsigned int>&, double)': bogus/bogusUtil.C:226:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 226 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:274:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 274 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C: In function 'void loadReferenceSequence(char*, std::vector&, std::map, unsigned int>&)': bogus/bogusUtil.C:300:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 300 | fgets(refhdr, 1024, F); chomp(refhdr); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:301:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 301 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:326:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(refhdr, 1024, F); chomp(refhdr); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bogus/bogusUtil.C:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 327 | fgets(refseq, MAX_GENOME_SIZE_INPUT, F); chomp(refseq); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from gfa/alignGFA.C:32: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu cp -pf pipelines/canu.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu cp -pf pipelines/canu-time.pl /build/canu-2.0+dfsg/Linux-i686/bin/canu-time chmod +x /build/canu-2.0+dfsg/Linux-i686/bin/canu-time echo > /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults "# Add site specific options (for setting up Grid or limiting memory/threads) here." chmod -x /build/canu-2.0+dfsg/Linux-i686/bin/canu.defaults cp -pf sequence/share/ultra-long-nanopore /build/canu-2.0+dfsg/Linux-i686/share/sequence/ultra-long-nanopore cp -pf sequence/share/pacbio /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio cp -pf sequence/share/pacbio-hifi /build/canu-2.0+dfsg/Linux-i686/share/sequence/pacbio-hifi gfa/alignGFA.C: In function 'bool checkRecord(bedRecord*, sequences&, sequences&, sequences&, bool, bool)': gfa/alignGFA.C:507:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 507 | success &= checkRecord_align("ALL", | ^~~~~ gfa/alignGFA.C:535:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 535 | success &= checkRecord_align("LEFT", | ^~~~~~ gfa/alignGFA.C:541:34: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 541 | success &= checkRecord_align("RIGHT", | ^~~~~~~ cp -pf pipelines/canu/Consensus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ gfa/alignGFA.C: In function 'void processBEDtoGFA(char*, uint32, char*, char*, double, uint32)': gfa/alignGFA.C:782:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 782 | gfaFile *gfa = new gfaFile("H\tVN:Z:1.0"); | ^~~~~~~~~~~~~ cp -pf pipelines/canu/CorrectReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:162:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 162 | system(Pfile); | ~~~~~~^~~~~~~ cp -pf pipelines/canu/OverlapMhap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMMap.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapStore.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /build/canu-2.0+dfsg/Linux-i686/lib/site_perl/canu/ g++ -o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -fPIC -DNOBACKTRACE -I/build/canu-2.0+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap AS_global.C In file included from stores/tgTig.H:36, from stores/tgStore.H:43, from utgcns/unitigConsensus.H:67, from utgcns/unitigConsensus.C:74: utility/bits.H: In member function 'void stuffedBits::updateBlk(uint64)': utility/bits.H:791:44: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 791 | fprintf(stderr, "ERROR: _dataBlk = %lu _dataBlocksLen = %u\n", _dataBlk, _dataBlocksLen); | ~~^ ~~~~~~~~ | | | | long unsigned int uint64 {aka long long unsigned int} | %llu gfa/alignGFA.C:140:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] 140 | sprintf(Pname, "plot-%s-%s", Aname, Bname); | ^~ ~~~~~ In file included from /usr/include/stdio.h:906, from /build/canu-2.0+dfsg/src/AS_global.H:67, from gfa/alignGFA.C:30: In function 'int sprintf(char*, const char*, ...)', inlined from 'void dotplot(uint32, bool, char*, uint32, bool, char*)' at gfa/alignGFA.C:140:10: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 8199 bytes into a destination of size 4097 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:141:24: warning: '%s' directive writing up to 4096 bytes into a region of size 4092 [-Wformat-overflow=] 141 | sprintf(Pfile, "plot-%s-%s.sh", Aname, Bname); | ^~ ~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void dotplot(uint32, bool, char*, uint32, bool, char*)' at gfa/alignGFA.C:141:10: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 8202 bytes into a destination of size 4097 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': gfa/alignGFA.C:160:27: warning: '%s' directive writing up to 4096 bytes into a region of size 4089 [-Wformat-overflow=] 160 | sprintf(Pfile, "sh plot-%s-%s.sh", Aname, Bname); | ^~ ~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void dotplot(uint32, bool, char*, uint32, bool, char*)' at gfa/alignGFA.C:160:10: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 13 and 8205 bytes into a destination of size 4097 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ar rv /build/canu-2.0+dfsg/Linux-i686/lib/libcanu.a /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/AS_global.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/edlib.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-buffered.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-compressed.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/files-memoryMapped.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/logging.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/strings.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/system-stackTrace.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sequence.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-reader.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-block.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-writer-stream.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-statistics.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/kmers-exact.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/bits.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/hexDump.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/md5.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/mt19937ar.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/objectStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/speedCounter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/utility/sweatShop.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqCache.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqLibrary.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadData.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovOverlap.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStore.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreFile.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/canu-2.0+dfsg/Linux-i686/obj/lib/libcanu.a/stores/tgStore.o 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-L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreIndexer -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreDump/stores/ovStoreDump.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/ovStoreStats -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/ovStoreStats/stores/ovStoreStats.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sqStoreCreate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib 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-L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/loadTrimmedReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/loadErates -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/loadErates/stores/loadErates.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/meryl.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylCountArray.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylInput.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-count.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-countSimple.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-histogram.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp-nextMer.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl/meryl/merylOp.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl-import -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/meryl-import.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-import/meryl/merylCountArray.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/meryl-lookup -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/meryl-lookup/meryl/meryl-lookup.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/sequence -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-extract.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-generate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-mutate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-sample.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-emit-fast.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-fast.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-shiftregister-search-slow.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-simulate.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/sequence/sequence/sequence-summarize.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapInCore -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapInCorePartition -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapImport -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapImport/overlapInCore/overlapImport.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapPair -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapPair/overlapInCore/overlapPair.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/edalign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/edalign/overlapInCore/edalign.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/prefixEditDistance-matchLimitGenerate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mhapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mhapConvert/mhap/mhapConvert.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mmapConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mmapConvert/minimap/mmapConvert.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/wtdbgConvert -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/generateCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/filterCorrectionLayouts -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/falconsense -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/correction/falconsense.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/falconsense/utgcns/stashContains.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/errorEstimate -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/errorEstimate/correction/errorEstimate.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitHaplotype -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/trimReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/splitReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/bogart.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigGraph.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/bogus -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogus.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/bogus/bogus/bogusUtil.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/alignGFA/gfa/alignGFA.o -lcanu g++ -o /build/canu-2.0+dfsg/Linux-i686/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-2.0+dfsg/Linux-i686/lib /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/utgcns.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/stashContains.o /build/canu-2.0+dfsg/Linux-i686/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu Success! canu installed in /build/canu-2.0+dfsg/Linux-i686/bin/canu make[2]: Leaving directory '/build/canu-2.0+dfsg/src' builddir=*-*/; \ find $builddir \ -name OverlapMhap.pm \ -exec sed -i 's#\(\s*my \$javaPath = \).*#\1 "/usr/lib/jvm/java-8-openjdk-i386/bin/java";#' {} + make[1]: Leaving directory '/build/canu-2.0+dfsg' dh_auto_test -O--sourcedirectory=src/ create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src/ dh_testroot -O--sourcedirectory=src/ dh_prep -O--sourcedirectory=src/ dh_auto_install --destdir=debian/canu/ -O--sourcedirectory=src/ debian/rules override_dh_install make[1]: Entering directory '/build/canu-2.0+dfsg' dh_install for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/canu-2.0+dfsg' dh_installdocs -O--sourcedirectory=src/ dh_installchangelogs -O--sourcedirectory=src/ dh_installman -O--sourcedirectory=src/ dh_installsystemduser -O--sourcedirectory=src/ dh_perl -O--sourcedirectory=src/ dh_link -O--sourcedirectory=src/ dh_strip_nondeterminism -O--sourcedirectory=src/ dh_compress -O--sourcedirectory=src/ dh_fixperms -O--sourcedirectory=src/ dh_missing -O--sourcedirectory=src/ dh_dwz -a -O--sourcedirectory=src/ dh_strip -a -O--sourcedirectory=src/ dh_makeshlibs -a -O--sourcedirectory=src/ dh_shlibdeps -a -O--sourcedirectory=src/ dh_installdeb -O--sourcedirectory=src/ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.0+dfsg-2_i386.deb'. dpkg-deb: building package 'canu' in '../canu_2.0+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../canu_2.0+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../canu_2.0+dfsg-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/30765/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/30765/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/30765 and its subdirectories I: Current time: Wed Apr 19 05:55:47 +14 2023 I: pbuilder-time-stamp: 1681833347