Thu Jul 8 20:38:07 UTC 2021 I: starting to build snap-aligner/bullseye/arm64 on jenkins on '2021-07-08 20:37' Thu Jul 8 20:38:07 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_30/10962/console.log Thu Jul 8 20:38:08 UTC 2021 I: Downloading source for bullseye/snap-aligner=1.0.0+dfsg-2 --2021-07-08 20:38:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_1.0.0+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2243 (2.2K) Saving to: ‘snap-aligner_1.0.0+dfsg-2.dsc’ 0K .. 100% 14.1M=0s 2021-07-08 20:38:08 (14.1 MB/s) - ‘snap-aligner_1.0.0+dfsg-2.dsc’ saved [2243/2243] Thu Jul 8 20:38:08 UTC 2021 I: snap-aligner_1.0.0+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snap-aligner Binary: snap-aligner Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64 riscv64 sparc64 Version: 1.0.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Pranav Ballaney Homepage: http://snap.cs.berkeley.edu/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man, zlib1g-dev, libsimde-dev Package-List: snap-aligner deb science optional arch=amd64,arm64,mips64el,ppc64el,s390x,alpha,kfreebsd-amd64,ppc64,riscv64,sparc64 Checksums-Sha1: 9d96d8672316ad4f1cab5c4dcfa5b7e281223ee7 1060724 snap-aligner_1.0.0+dfsg.orig.tar.xz 004cc0359a6746ad47a0cb8854e0921c72e2bce6 8976 snap-aligner_1.0.0+dfsg-2.debian.tar.xz Checksums-Sha256: 64e1eb4758b067c372e9ff41daabaefec5c8ebff4996fe595b9be67d916c4b3c 1060724 snap-aligner_1.0.0+dfsg.orig.tar.xz cddd8dcedfccbf16135e438dc976ac2bec8f606f8fa362313516913e66d328ca 8976 snap-aligner_1.0.0+dfsg-2.debian.tar.xz Files: 583e2df4d5b18c8a5c81bd00d83bb66c 1060724 snap-aligner_1.0.0+dfsg.orig.tar.xz a0de0fbb8f95a7aa60829a2e5eb51039 8976 snap-aligner_1.0.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl/DaOMACgkQPCZ2P2xn 5uLqfQ/8CS9sc5LiLnjn2sA2geFpGWoEGWsVBytOGLYuPEFv1X4hsvGxfbcagL9I QI6Il7RRIuOgnADtQyXs5JuWi94/sMqq4BgUR/wYMvRwFjMX0F6RznzBl2/Rdc4k d+4VUSpM3cDZMM3WKFj8w6NIjcpgiHm4z51F/94mut4IP0QQCBYhQP4I2hApCARw pgX9I7GdF9ruFSyuelg4WsWQFP/4XxqsFRgVREAp21hpP1A8LsxLfOf+pKGWqyvQ +7AStQVMR6QuV+g8bwPE8U5X5n8HN/QJdThSbG5AO7gQs2H8lIeNq42Rctezn+y7 h3ebASN1eGM8jojxg93euvXHMiZF2sv+1q3VEw5UvATWb5ybhmNsnVZHPPEkycvT 8Q/T4OKrav7dKLT1uG5TOT2vpr42IXVnXzqbAELJvj/YyzhwAAPYavD8UdGueaFP 8kP/yE87oa6T9p8+XzyuknfFrB/pJPakXtj+6qzQAS6pZDr9GygIxwgw6NnjoTL6 NWSaYvbE/aEfnEBscsBlyAs6oFgAWOJJr4VLk5DEHB+Qzo/jPclEPxF6xyqkU+HJ 9tlIvUSfMk4NQ9NmHt4g2hFIOdxQPT30A8fEVHcz161vawV9ZmThOqCjkSiC+LqH LGgUkwlkjInBeBH4FazliQAM0zUizabo5Rj5g9ti/0MBYrIh1kU= =pF+c -----END PGP SIGNATURE----- Thu Jul 8 20:38:08 UTC 2021 I: Checking whether the package is not for us Thu Jul 8 20:38:08 UTC 2021 I: Starting 1st build on remote node codethink16-arm64.debian.net. Thu Jul 8 20:38:08 UTC 2021 I: Preparing to do remote build '1' on codethink16-arm64.debian.net. Thu Jul 8 20:40:44 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 8 08:38:11 -12 2021 I: pbuilder-time-stamp: 1625776691 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: Copying source file I: copying [snap-aligner_1.0.0+dfsg-2.dsc] I: copying [./snap-aligner_1.0.0+dfsg.orig.tar.xz] I: copying [./snap-aligner_1.0.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.0A3VuJp3/trustedkeys.kbx': General error gpgv: Signature made Sat Nov 28 21:24:51 2020 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./snap-aligner_1.0.0+dfsg-2.dsc dpkg-source: info: extracting snap-aligner in snap-aligner-1.0.0+dfsg dpkg-source: info: unpacking snap-aligner_1.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking snap-aligner_1.0.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_segfault.patch dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying spelling dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20098/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='20098' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/pbuilderrc_58xp --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/b1 --logfile b1/build.log snap-aligner_1.0.0+dfsg-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink16-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 7 21:24 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/20098/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: arm64 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), help2man, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 18.6 MB of archives. After unpacking 72.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsimde-dev all 0.7.2-4 [259 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 18.6 MB in 0s (52.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../24-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../26-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package help2man. Preparing to unpack .../32-help2man_1.48.1_arm64.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../33-libsimde-dev_0.7.2-4_all.deb ... Unpacking libsimde-dev (0.7.2-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../34-zlib1g-dev_1%3a1.2.11.dfsg-2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up libsimde-dev (0.7.2-4) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... 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 I: Building the package I: Running cd /build/snap-aligner-1.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snap-aligner_1.0.0+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 1.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' dh_auto_clean make -j8 clean make[2]: Entering directory '/build/snap-aligner-1.0.0+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/snap-aligner-1.0.0+dfsg' g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp In file included from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerStats.h:29, from SNAPLib/AlignerStats.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignerOptions.h:29, from SNAPLib/AlignerOptions.cpp:28: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.cpp:2: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.cpp:2: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.cpp:2: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/ApproximateCounter.cpp:3: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/AlignmentResult.cpp:23: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/AlignerContext.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerContext.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AlignerContext.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerContext.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AlignerContext.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AlignerContext.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.cpp:2: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.cpp:2: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.cpp:2: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/GenomeIndex.h:27, from SNAPLib/AlignmentAdjuster.h:27, from SNAPLib/AlignmentAdjuster.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp In file included from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.h:22, from SNAPLib/Bam.cpp:20: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/BaseAligner.cpp:29: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | SNAPLib/AlignerContext.cpp: In member function 'void AlignerContext::printStats()': SNAPLib/AlignerContext.cpp:486:75: warning: format '%lld' expects argument of type 'long long int', but argument 9 has type '_int64' {aka 'long int'} [-Wformat=] 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", | ~~~^ | | | long long int | %ld ...... 492 | stats->lvCalls, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/AlignerContext.cpp:486:90: warning: format '%lld' expects argument of type 'long long int', but argument 11 has type '_int64' {aka 'long int'} [-Wformat=] 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", | ~~~^ | | | long long int | %ld ...... 494 | stats->totalReads, | ~~~~~~~~~~~~~~~~~ | | | _int64 {aka long int} In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BigAlloc.cpp:24: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BigAlloc.cpp:24: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BigAlloc.cpp:24: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/ChimericPairedEndAligner.h:27, from SNAPLib/ChimericPairedEndAligner.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BufferedAsync.cpp:21: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BufferedAsync.cpp:21: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/BufferedAsync.cpp:21: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Compat.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Compat.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Compat.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataReader.cpp:22: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataReader.cpp:22: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataReader.cpp:22: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataWriter.cpp:21: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataWriter.cpp:21: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/DataWriter.cpp:21: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp In file included from SNAPLib/Error.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Error.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Error.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp In file included from SNAPLib/FASTA.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTA.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/FASTA.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTA.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/FASTA.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTA.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:1751:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 1751 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:1755:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 1755 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:1759:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 1759 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': SNAPLib/DataReader.cpp:1900:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 1900 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:1900:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 1900 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:1904:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 1904 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': SNAPLib/Error.cpp:89:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 89 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); | ~~~^ ~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_map.h:26, from SNAPLib/GenericFile_map.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/GenericFile_stdio.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile_stdio.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/GenericFile_stdio.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile_stdio.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/GenericFile_stdio.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GenericFile_stdio.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/GzipDataWriter.h:25, from SNAPLib/GzipDataWriter.cpp:20: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:419:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 419 | fprintf(stderr,"%llds\n", (timeInMillis() + 500 - start) / 1000); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/GenomeIndex.cpp:794:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:794:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:794:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:849:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 849 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 850 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | _uint64 {aka long unsigned int} SNAPLib/GenomeIndex.cpp:849:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 849 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 850 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:164:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] 164 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, (areALTContigsMarked ? GENOME_FLAG_ALT_CONTIGS_MARKED : 0)); | ~~~^ ~~~~~~ | | | | | long int | long long int | %ld SNAPLib/Genome.cpp:174:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 174 | fprintf(saveFile, "%lld %x %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), contigs[i].name); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp:176:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 176 | fprintf(saveFile, "%lld %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), contigs[i].name); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:267:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] 267 | if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) { | ~~~^ ~~~~~~~~~~~~ | | | | | _int64* {aka long int*} | long long int* | %ld SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool, bool*)': SNAPLib/Genome.cpp:401:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] 401 | if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) { | ~~~^ ~~~~~~ | | | | | GenomeDistance* {aka long int*} | long long int* | %ld SNAPLib/Genome.cpp:410:31: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] 410 | if (3 == sscanf(linebuf, "%lld %d %d\n", nBases, nContigs, &flags)) | ~~~^ ~~~~~~ | | | | | GenomeDistance* {aka long int*} | long long int* | %ld SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1707:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1707 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/GenomeIndex.cpp:1707:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] 1707 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ | | | long long int* | %ld 1708 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) { | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} In file included from SNAPLib/Histogram.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Histogram.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Histogram.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Histogram.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Histogram.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Histogram.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/HashTable.h:23, from SNAPLib/HashTable.cpp:20: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.h:25, from SNAPLib/IntersectingPairedEndAligner.cpp:24: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.cpp:2: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.cpp:2: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.cpp:2: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/PairedAligner.cpp:34: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedAligner.cpp:34: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/PairedAligner.cpp:34: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedAligner.cpp:34: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/PairedAligner.cpp:34: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedAligner.cpp:34: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedReadMatcher.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedReadMatcher.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/PairedReadMatcher.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ParallelTask.h:25, from SNAPLib/ParallelTask.cpp:18: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ProbabilityDistance.h:3, from SNAPLib/ProbabilityDistance.cpp:2: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' SNAPLib/PairedAligner.cpp: In member function 'virtual void PairedAlignerContext::runIterationThread()': SNAPLib/PairedAligner.cpp:618:68: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 618 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu In file included from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadReader.cpp:19: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadReader.cpp:19: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadReader.cpp:19: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Read.h:28, from SNAPLib/ReadSupplierQueue.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] 44 | } | ^ g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp In file included from SNAPLib/ReadWriter.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadWriter.cpp:21: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/ReadWriter.cpp:21: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadWriter.cpp:21: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/ReadWriter.cpp:21: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/ReadWriter.cpp:21: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp In file included from SNAPLib/SAM.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.cpp:21: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/SAM.cpp:21: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.cpp:21: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/SAM.cpp:21: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SAM.cpp:21: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/Seed.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, from SNAPLib/SingleAligner.cpp:27: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1247:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] 1247 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu\n", contigs[i].name, end - start); | ~~~^ ~~~~~~~~~~~ | | | | long long unsigned int GenomeLocation {aka long int} | %lu SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, int*, int*, bool*, bool*) const': SNAPLib/SAM.cpp:1957:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1957 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1961 | positionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:1957:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1957 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1965 | matePositionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2153:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2157 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2153:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2161 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2153:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long int | %ld ...... 2162 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2358:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2362 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2358:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2366 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2358:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | ~~~^ | | | long long int | %ld ...... 2367 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2687:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu In file included from SNAPLib/SortedDataWriter.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SortedDataWriter.cpp:21: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/SortedDataWriter.cpp:21: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SortedDataWriter.cpp:21: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/SortedDataWriter.cpp:21: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/SortedDataWriter.cpp:21: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | SNAPLib/SAM.cpp:2690:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2777:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2780:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThread()': SNAPLib/SingleAligner.cpp:181:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 181 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu In file included from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/Util.h:5, from SNAPLib/Util.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/mapq.cpp:25: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/mapq.cpp:25: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/mapq.cpp:25: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1183:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1183 | commandLine[0] = '\0'; | ~~~~~~~~~~~~~~~^~~~~~ SNAPLib/SAM.cpp:1182:40: note: at offset 0 to an object with size 0 allocated by 'operator new []' here 1182 | commandLine = new char[commandLineSize]; | ^ In file included from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp In file included from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGap.h:3, from tests/AffineGapTest.cpp:3: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:166:28: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 166 | sprintf(tempBuf, ",%03lld", x % 1000); | ~~~~~^ ~~~~~~~~ | | | | | _uint64 {aka long unsigned int} | long long int | %03ld SNAPLib/Util.cpp:169:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 169 | sprintf(tempBuf, "%lld", x); | ~~~^ ~ | | | | | _uint64 {aka long unsigned int} | long long int | %ld g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp In file included from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/EventTest.cpp:3: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/AffineGapVectorized.h:3, from tests/AffineGapVectorizedTest.cpp:3: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | In file included from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp In file included from tests/ProbabilityDistanceTest.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from tests/ProbabilityDistanceTest.cpp:2: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from tests/ProbabilityDistanceTest.cpp:2: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from tests/ProbabilityDistanceTest.cpp:2: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from tests/ProbabilityDistanceTest.cpp:2: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from tests/ProbabilityDistanceTest.cpp:2: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2687:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2687:54: note: directive argument in the range [1, 9223372036854775807] 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp:2690:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2690:52: note: directive argument in the range [1, 9223372036854775807] 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2777:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2777:54: note: directive argument in the range [1, 9223372036854775807] 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp:2780:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2780:52: note: directive argument in the range [1, 9223372036854775807] 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp In file included from apps/SNAPCommand/SNAPCommand.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from apps/SNAPCommand/SNAPCommand.cpp:26: /usr/include/simde/x86/sse.h:3294: note: this is the location of the previous definition 3294 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | In file included from apps/SNAPCommand/SNAPCommand.cpp:26: SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from apps/SNAPCommand/SNAPCommand.cpp:26: /usr/include/simde/x86/sse.h:3296: note: this is the location of the previous definition 3296 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 | In file included from apps/SNAPCommand/SNAPCommand.cpp:26: SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81, from apps/SNAPCommand/SNAPCommand.cpp:26: /usr/include/simde/x86/sse.h:3298: note: this is the location of the previous definition 3298 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -o snap-aligner -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz g++ -o unit_tests -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz make[2]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' help2man --no-discard-stderr --no-info --version-string="1.0.0" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="1.0.0" \ --include=debian/snap-aligner-${option}-man-include \ --help-option=" " "./snap-aligner ${option}" > \ debian/snap-aligner-${option}.1; done help2man --no-discard-stderr --no-info --version-string="1.0.0" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' dh_auto_test ./unit_tests AffineGapTest: - synthetic: [OK] AffineGapVectorizedTest: - equal strings: [OK] - one deletion: [OK] - long deletion: [OK] - long insertion: [OK] - synthetic: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] 15 / 15 tests passed. make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snap-aligner' in '../snap-aligner_1.0.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snap-aligner_1.0.0+dfsg-2_arm64.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: 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/20098 and its subdirectories I: Current time: Thu Jul 8 08:40:43 -12 2021 I: pbuilder-time-stamp: 1625776843 Thu Jul 8 20:40:45 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Thu Jul 8 20:40:45 UTC 2021 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Thu Jul 8 20:43:23 UTC 2021 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Thu Jul 8 20:43:24 UTC 2021 I: snap-aligner_1.0.0+dfsg-2_arm64.changes: Format: 1.8 Date: Sun, 29 Nov 2020 10:24:29 +0100 Source: snap-aligner Binary: snap-aligner snap-aligner-dbgsym Architecture: arm64 Version: 1.0.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: snap-aligner - Scalable Nucleotide Alignment Program Changes: snap-aligner (1.0.0+dfsg-2) unstable; urgency=medium . * debian/rules: The file in the examples folder with the incorrect execute bit is from the debian/ directory, so fix the permission there instead of the hack previously used. Checksums-Sha1: 7ba0b6d77c335e3c811eb83b5de025ee8ffbbdf0 2262904 snap-aligner-dbgsym_1.0.0+dfsg-2_arm64.deb a5b48c2d938ec1386101fb867d078f2f665aa532 5038 snap-aligner_1.0.0+dfsg-2_arm64.buildinfo 822a57a2d40e27416fc57b1e5606844738cb1d84 745148 snap-aligner_1.0.0+dfsg-2_arm64.deb Checksums-Sha256: 166a3ad236c9c5a8d31925c252f6a3a90986098b9e48534692a5b1ecbc804663 2262904 snap-aligner-dbgsym_1.0.0+dfsg-2_arm64.deb fe72b166de704f7438e1de5daef608e2ba7aa3422cf955a7128387280308a87c 5038 snap-aligner_1.0.0+dfsg-2_arm64.buildinfo 48e2efb0a6b0ec04ee7ed535783a4139676dd1ec3caf5cef5757d87c0214dacc 745148 snap-aligner_1.0.0+dfsg-2_arm64.deb Files: c11bdbe065a310541c99f1875105eb34 2262904 debug optional snap-aligner-dbgsym_1.0.0+dfsg-2_arm64.deb 3f82b5d834b3ecefae5e9675a9a8490c 5038 science optional snap-aligner_1.0.0+dfsg-2_arm64.buildinfo 84f3d17f131d860bbce3c5a93c592804 745148 science optional snap-aligner_1.0.0+dfsg-2_arm64.deb Thu Jul 8 20:43:25 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/snap-aligner_1.0.0+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/snap-aligner_1.0.0+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/snap-aligner_1.0.0+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/b1/snap-aligner_1.0.0+dfsg-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.dGRzCWb0qN/b2/snap-aligner_1.0.0+dfsg-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.379s) 0.379s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.068s) 0.068s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jul 8 20:43:27 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 8 20:43:27 UTC 2021 I: snap-aligner from bullseye built successfully and reproducibly on arm64. Thu Jul 8 20:43:29 UTC 2021 I: Submitting .buildinfo files to external archives: Thu Jul 8 20:43:29 UTC 2021 I: Submitting 8.0K b1/snap-aligner_1.0.0+dfsg-2_arm64.buildinfo.asc Thu Jul 8 20:43:30 UTC 2021 I: Submitting 8.0K b2/snap-aligner_1.0.0+dfsg-2_arm64.buildinfo.asc Thu Jul 8 20:43:31 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 8 20:43:31 UTC 2021 I: Done submitting .buildinfo files. Thu Jul 8 20:43:31 UTC 2021 I: Removing signed snap-aligner_1.0.0+dfsg-2_arm64.buildinfo.asc files: removed './b1/snap-aligner_1.0.0+dfsg-2_arm64.buildinfo.asc' removed './b2/snap-aligner_1.0.0+dfsg-2_arm64.buildinfo.asc'