Diff of the two buildlogs: -- --- b1/build.log 2023-04-29 13:16:46.788937318 +0000 +++ b2/build.log 2023-04-29 13:25:42.233433120 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 31 07:37:36 -12 2024 -I: pbuilder-time-stamp: 1717184256 +I: Current time: Sun Apr 30 03:16:49 +14 2023 +I: pbuilder-time-stamp: 1682774209 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.7DTfRfTT/trustedkeys.kbx': General error -gpgv: Signature made Sun Jan 8 18:59:16 2023 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.QuK5KvmZ/trustedkeys.kbx': General error +gpgv: Signature made Mon Jan 9 20:59:16 2023 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -28,135 +28,166 @@ dpkg-source: info: unpacking macromoleculebuilder_3.2+dfsg-2+deb11u1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4106802/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 30 03:17 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3869859/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='373716bb6c384ddebbf2255e813882f8' - 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='4106802' - PS1='# ' - PS2='> ' + INVOCATION_ID=bb6fb9c52a4444db95812a5fcbd97c92 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3869859 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/r-b-build.mSmvXjLf/pbuilderrc_lrEy --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/b1 --logfile b1/build.log macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/pbuilderrc_KvGQ --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mSmvXjLf/b2 --logfile b2/build.log macromoleculebuilder_3.2+dfsg-2+deb11u1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 May 23 03:55 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/4106802/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 22:23 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 22:23 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 22:23 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Apr 30 03:17 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -374,7 +405,7 @@ Get: 164 http://deb.debian.org/debian bullseye/main amd64 libsimbody-dev amd64 3.6.1+dfsg-7 [2726 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libsimtkmolmodel3.0 amd64 3.0~svn842-2 [532 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libsimtkmolmodel-dev amd64 3.0~svn842-2 [1858 kB] -Fetched 97.3 MB in 1s (77.0 MB/s) +Fetched 97.3 MB in 6s (16.9 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 ... 19707 files and directories currently installed.) @@ -1065,7 +1096,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/macromoleculebuilder-3.2+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 > ../macromoleculebuilder_3.2+dfsg-2+deb11u1_source.changes +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/macromoleculebuilder-3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../macromoleculebuilder_3.2+dfsg-2+deb11u1_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 3.2+dfsg-2+deb11u1 dpkg-buildpackage: info: source distribution bullseye @@ -1113,7 +1148,7 @@ -- Build files have been written to: /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/macromoleculebuilder-3.2+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/macromoleculebuilder-3.2+dfsg -B/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1129,37 +1164,35 @@ make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build make[3]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMBlib.dir/src/Utils.cpp.o -[ 6%] Building CXX object CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o -[ 10%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o -[ 13%] Building CXX object CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -[ 17%] Building CXX object CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o -[ 20%] Building CXX object CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o -[ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o -[ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o -[ 31%] Building CXX object CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o -[ 34%] Building CXX object CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Utils.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp +[ 6%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp +[ 10%] Building CXX object CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp +[ 13%] Building CXX object CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp -[ 37%] Building CXX object CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o +[ 17%] Building CXX object CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp +[ 20%] Building CXX object CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MobilizerContainer.cpp +[ 24%] Building CXX object CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o +[ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp -[ 41%] Building CXX object CMakeFiles/MMBlib.dir/src/Repel.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp +[ 31%] Building CXX object CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp -[ 44%] Building CXX object CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o -[ 48%] Building CXX object CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o -[ 51%] Building CXX object CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o +[ 34%] Building CXX object CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Repel.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp +[ 37%] Building CXX object CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp +[ 41%] Building CXX object CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp +[ 44%] Building CXX object CMakeFiles/MMBlib.dir/src/Repel.cpp.o +[ 48%] Building CXX object CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o +[ 51%] Building CXX object CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Repel.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp -[ 55%] Building CXX object CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp: In member function 'const double UnitCellParameters::angleInRange(double)': /build/macromoleculebuilder-3.2+dfsg/src/UnitCellParameters.cpp:165:2: warning: control reaches end of non-void function [-Wreturn-type] 165 | } @@ -1169,22 +1202,36 @@ 270 | } | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp:12: + from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, + from /build/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:17: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:16, - from /build/macromoleculebuilder-3.2+dfsg/include/Repel.h:21, - from /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:12: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, + from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, + from /build/macromoleculebuilder-3.2+dfsg/include/DensityContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:11: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, + from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, + from /build/macromoleculebuilder-3.2+dfsg/include/DisplacementContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ +In file included from /build/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp:10: +/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' + 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") + | ^ +In file included from /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp:11: +/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' + 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") + | ^ +[ 55%] Building CXX object CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp In file included from /build/macromoleculebuilder-3.2+dfsg/src/MobilizerContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") @@ -1195,78 +1242,69 @@ /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/BaseInteractionParameterReader.h:22, - from /build/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp:16: -/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' - 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") - | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/TetherForce.h:20, - from /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp:11: -/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' - 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") - | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, - from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, - from /build/macromoleculebuilder-3.2+dfsg/include/BasePairContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:11: + from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicScrubber.h:16, + from /build/macromoleculebuilder-3.2+dfsg/include/Repel.h:21, + from /build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -[ 58%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, - from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, - from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:13: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/BaseInteractionParameterReader.h:22, + from /build/macromoleculebuilder-3.2+dfsg/src/BaseInteractionParameterReader.cpp:16: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp -In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, - from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, - from /build/macromoleculebuilder-3.2+dfsg/include/DensityContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/src/DensityContainer.cpp:11: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/src/AtomSpringContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, - from /build/macromoleculebuilder-3.2+dfsg/include/DisplacementContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:12: + from /build/macromoleculebuilder-3.2+dfsg/include/BasePairContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/ConstraintContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/src/ConstraintContainer.cpp:10: +/build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': +/build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:127:49: note: '#pragma message: USE_OPENMM is defined' + 127 | #pragma message ("USE_OPENMM is defined") + | ^ +In file included from /build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/src/ParameterReader.cpp:17: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, + from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, + from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:13: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -/build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': -/build/macromoleculebuilder-3.2+dfsg/src/Repel.cpp:127:49: note: '#pragma message: USE_OPENMM is defined' - 127 | #pragma message ("USE_OPENMM is defined") - | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::setRenumberPdbResidues(bool)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:1067:5: warning: no return statement in function returning non-void [-Wreturn-type] 1067 | } | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/src/ContactContainer.cpp:11: -/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' - 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") - | ^ +/build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp: In member function 'Displacement& DisplacementContainer::updDisplacement(SimTK::String)': +/build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:41:1: warning: control reaches end of non-void function [-Wreturn-type] + 41 | }; + | ^ /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClassContainer::setRenumberPdbResidues(bool)': /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp:4725:1: warning: no return statement in function returning non-void [-Wreturn-type] 4725 | } | ^ +/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'const int MonoAtoms::getResidueIndex(ResidueID)': +/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:153:1: warning: control reaches end of non-void function [-Wreturn-type] + 153 | } + | ^ +/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'MonoAtoms MonoAtomsContainer::getMonoAtoms(SimTK::String)': +/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:277:1: warning: control reaches end of non-void function [-Wreturn-type] + 277 | } + | ^ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'SimTK::Compound CompoundObjectMapContainer::fetchCompound(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:73:1: warning: control reaches end of non-void function [-Wreturn-type] 73 | } @@ -1283,44 +1321,20 @@ /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type] 244 | } | ^ +[ 58%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp: In member function 'bool MoleculeClassContainer::hasChainID(SimTK::String)': /build/macromoleculebuilder-3.2+dfsg/src/MoleculeContainer.cpp:722:1: warning: control reaches end of non-void function [-Wreturn-type] 722 | } | ^ -/build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp: In function 'int ValidateNonNegativeInt(int)': -/build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:526:1: warning: control reaches end of non-void function [-Wreturn-type] - 526 | } - | ^ -/build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp: In member function 'Displacement& DisplacementContainer::updDisplacement(SimTK::String)': -/build/macromoleculebuilder-3.2+dfsg/src/DisplacementContainer.cpp:41:1: warning: control reaches end of non-void function [-Wreturn-type] - 41 | }; - | ^ -/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'const int MonoAtoms::getResidueIndex(ResidueID)': -/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:153:1: warning: control reaches end of non-void function [-Wreturn-type] - 153 | } - | ^ -/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp: In member function 'MonoAtoms MonoAtomsContainer::getMonoAtoms(SimTK::String)': -/build/macromoleculebuilder-3.2+dfsg/src/MonoAtoms.cpp:277:1: warning: control reaches end of non-void function [-Wreturn-type] - 277 | } - | ^ +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp [ 62%] Building CXX object CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp [ 65%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp -[ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp -[ 72%] Building CXX object CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp -[ 75%] Building CXX object CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp -[ 79%] Building CXX object CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp -[ 82%] Building CXX object CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'bool BasePairContainer::hasWatsonCrickCisPair(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:184:1: warning: control reaches end of non-void function [-Wreturn-type] 184 | } | ^ -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NTC_PARAMETER_READER.cpp /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp: In member function 'const BaseInteraction BasePairContainer::getWatsonCrickCisPair(SimTK::String, ResidueID)': /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:206:1: warning: control reaches end of non-void function [-Wreturn-type] 206 | } // of method @@ -1337,14 +1351,28 @@ /build/macromoleculebuilder-3.2+dfsg/src/BasePairContainer.cpp:289:1: warning: control reaches end of non-void function [-Wreturn-type] 289 | } // of getLastWatsonCrickCisPairingResidueOfRun | ^ -[ 86%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp +[ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp +/build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp: In function 'int ValidateNonNegativeInt(int)': +/build/macromoleculebuilder-3.2+dfsg/src/Utils.cpp:526:1: warning: control reaches end of non-void function [-Wreturn-type] + 526 | } + | ^ +[ 72%] Building CXX object CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp +[ 75%] Building CXX object CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp +[ 79%] Building CXX object CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp: In member function 'ErrorManager& ErrorManager::operator=(const ErrorManager&)': /build/macromoleculebuilder-3.2+dfsg/src/ErrorManager.cpp:25:1: warning: no return statement in function returning non-void [-Wreturn-type] 24 | _buffer << em._buffer.rdbuf(); +++ |+ return *this; 25 | } | ^ +[ 82%] Building CXX object CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NTC_PARAMETER_READER.cpp +[ 86%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o +/usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp [ 89%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/build/macromoleculebuilder-3.2+dfsg/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/build/macromoleculebuilder-3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -c /build/macromoleculebuilder-3.2+dfsg/src/NtCForces.cpp /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::validateBiopolymerType() const': @@ -1393,20 +1421,28 @@ | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClassTwoTransformForces.h:18, - from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: + from /build/macromoleculebuilder-3.2+dfsg/include/TetherForce.h:20, + from /build/macromoleculebuilder-3.2+dfsg/src/TetherForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:16, - from /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:11: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, + from /build/macromoleculebuilder-3.2+dfsg/include/DensityForce.h:20, + from /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/ElectrostaticPotentialGridForce.h:20, - from /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: + from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClassTwoTransformForces.h:18, + from /build/macromoleculebuilder-3.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: +/build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' + 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") + | ^ +In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, + from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, + from /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp:12: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ @@ -1417,27 +1453,26 @@ /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:11: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/WaterDroplet.h:16, + from /build/macromoleculebuilder-3.2+dfsg/src/WaterDroplet.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, - from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, - from /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:15: +In file included from /build/macromoleculebuilder-3.2+dfsg/src/DensityMap.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, - from /build/macromoleculebuilder-3.2+dfsg/include/DensityForce.h:20, - from /build/macromoleculebuilder-3.2+dfsg/src/DensityForce.cpp:11: + from /build/macromoleculebuilder-3.2+dfsg/include/ElectrostaticPotentialGridForce.h:20, + from /build/macromoleculebuilder-3.2+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ -In file included from /build/macromoleculebuilder-3.2+dfsg/include/Mutation.h:4, - from /build/macromoleculebuilder-3.2+dfsg/include/BiopolymerClass.h:18, - from /build/macromoleculebuilder-3.2+dfsg/src/NtCClassContainer.cpp:12: +In file included from /build/macromoleculebuilder-3.2+dfsg/include/AtomSpringContainer.h:14, + from /build/macromoleculebuilder-3.2+dfsg/include/ParameterReader.h:20, + from /build/macromoleculebuilder-3.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, + from /build/macromoleculebuilder-3.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:15: /build/macromoleculebuilder-3.2+dfsg/include/Utils.h:33:70: note: '#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined' 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ @@ -1499,7 +1534,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/macromoleculebuilder-3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/macromoleculebuilder-3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/macromoleculebuilder-3.2+dfsg -B/build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/macromoleculebuilder-3.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1704,12 +1739,12 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libmmblib-dev' in '../libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb'. -dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. -dpkg-deb: building package 'libmmblib3.2-dbgsym' in '../libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. +dpkg-deb: building package 'libmmblib3.2' in '../libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'mmb' in '../mmb_3.2+dfsg-2+deb11u1_amd64.deb'. +dpkg-deb: building package 'libmmblib3.2-dbgsym' in '../libmmblib3.2-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. +dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-deb: building package 'mmb-common' in '../mmb-common_3.2+dfsg-2+deb11u1_all.deb'. -dpkg-deb: building package 'libmmblib3.2' in '../libmmblib3.2_3.2+dfsg-2+deb11u1_amd64.deb'. +dpkg-deb: building package 'libmmblib-dev' in '../libmmblib-dev_3.2+dfsg-2+deb11u1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../macromoleculebuilder_3.2+dfsg-2+deb11u1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1717,12 +1752,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3869859/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/4106802 and its subdirectories -I: Current time: Fri May 31 07:39:46 -12 2024 -I: pbuilder-time-stamp: 1717184386 +I: removing directory /srv/workspace/pbuilder/3869859 and its subdirectories +I: Current time: Sun Apr 30 03:25:41 +14 2023 +I: pbuilder-time-stamp: 1682774741