Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/probcons/probcons_1.12-13_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/probcons-1.12-138rloioqy/probcons_1.12-13_amd64.buildinfo Get source package info: probcons=1.12-13 Source URL: http://snapshot.notset.fr/mr/package/probcons/1.12-13/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-17 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblkid1=2.36-3+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.182-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libicu67=67.1-4 libisl22=0.22.1-1 libitm1=10.2.0-17 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblsan0=10.2.0-17 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libquadmath0=10.2.0-17 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libsub-override-perl=0.09-2 libsystemd0=246.6-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d probcons=1.12-13 && mkdir -p /build/probcons-cynwzx && dpkg-source --no-check -x /*.dsc /build/probcons-cynwzx/probcons-1.12 && chown -R builduser:builduser /build/probcons-cynwzx" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/probcons-cynwzx/probcons-1.12 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605516358" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/probcons-cynwzx /tmp/probcons-1.12-138rloioqy bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.znflgZBG_x as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.znflgZBG_x Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1115 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4695 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.znflgZBG_x Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1129 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.znflgZBG_x I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d probcons=1.12-13 && mkdir -p /build/probcons-cynwzx && dpkg-source --no-check -x /*.dsc /build/probcons-cynwzx/probcons-1.12 && chown -R builduser:builduser /build/probcons-cynwzx"' exec /tmp/mmdebstrap.znflgZBG_x Reading package lists... NOTICE: 'probcons' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/probcons.git Please use: git clone https://salsa.debian.org/med-team/probcons.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 58.6 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main probcons 1.12-13 (dsc) [2049 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main probcons 1.12-13 (tar) [43.2 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main probcons 1.12-13 (diff) [13.4 kB] Fetched 58.6 kB in 0s (510 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'probcons_1.12-13.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting probcons in /build/probcons-cynwzx/probcons-1.12 dpkg-source: info: unpacking probcons_1.12.orig.tar.gz dpkg-source: info: unpacking probcons_1.12-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_add-RNA-in-Makefile.patch dpkg-source: info: applying 11-Rename-programs-in-Makefile.patch dpkg-source: info: applying fix-gcc-4.5-headers dpkg-source: info: applying fix-gcc-4.6.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/probcons-cynwzx/probcons-1.12 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605516358" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.znflgZBG_x dpkg-buildpackage: info: source package probcons dpkg-buildpackage: info: source version 1.12-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/build/probcons-cynwzx/probcons-1.12' rm -f probcons probcons-RNA pc-compare pc-project pc-makegnuplot make[1]: Leaving directory '/build/probcons-cynwzx/probcons-1.12' debian/rules override_dh_clean make[1]: Entering directory '/build/probcons-cynwzx/probcons-1.12' dh_clean probcons probcons-RNA pc-project pc-compare pc-makegnuplot Main-RNA.cc Defaults-RNA.h make[1]: Leaving directory '/build/probcons-cynwzx/probcons-1.12' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/probcons-cynwzx/probcons-1.12' cp Main.cc Main-RNA.cc sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc cp debian/Defaults-RNA.h Defaults-RNA.h dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/probcons-cynwzx/probcons-1.12' g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-cynwzx/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -lm -o probcons Main.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-cynwzx/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -lm -o probcons-RNA Main-RNA.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-cynwzx/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-compare CompareToRef.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-cynwzx/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Main-RNA.cc:8: Sequence.h: In member function ‘Sequence* Sequence::Clone() const’: Sequence.h:293:21: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Main-RNA.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = char]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, from CompareToRef.cc:9: Sequence.h: In member function ‘Sequence* Sequence::Clone() const’: Sequence.h:293:21: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from CompareToRef.cc:8: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = char]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, from Main.cc:8: Sequence.h: In member function ‘Sequence* Sequence::Clone() const’: Sequence.h:293:21: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Main.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = char]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, from ProjectPairwise.cc:9: Sequence.h: In member function ‘Sequence* Sequence::Clone() const’: Sequence.h:293:21: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from ProjectPairwise.cc:8: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = char]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Main.cc:11: ProbabilisticModel.h: In member function ‘void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const’: ProbabilisticModel.h:493:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ In file included from Main-RNA.cc:11: ProbabilisticModel.h: In member function ‘void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const’: ProbabilisticModel.h:493:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ ProbabilisticModel.h: In member function ‘VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const’: ProbabilisticModel.h:1027:18: warning: variable ‘postPtr’ set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ ProbabilisticModel.h: In member function ‘VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const’: ProbabilisticModel.h:1027:18: warning: variable ‘postPtr’ set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ Main.cc: In function ‘void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)’: Main.cc:282:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Main.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc:283:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Main.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc:284:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Main.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc: In function ‘MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)’: Main.cc:400:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) | ^~ Main.cc:403:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 403 | delete alignment.first; | ^~~~~~ Main.cc: In function ‘void ReadParameters()’: Main.cc:893:40: warning: implicitly-declared ‘SafeVector >& SafeVector >::operator=(const SafeVector >&)’ is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ In file included from Main.cc:7: SafeVector.h:29:3: note: because ‘SafeVector >’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Main.cc:894:29: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ In file included from Main.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = float]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Main-RNA.cc: In function ‘void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)’: Main-RNA.cc:282:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc:283:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc:284:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc: In function ‘MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)’: Main-RNA.cc:400:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) | ^~ Main-RNA.cc:403:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 403 | delete alignment.first; | ^~~~~~ Main-RNA.cc: In function ‘void ReadParameters()’: Main-RNA.cc:893:40: warning: implicitly-declared ‘SafeVector >& SafeVector >::operator=(const SafeVector >&)’ is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ In file included from Main-RNA.cc:7: SafeVector.h:29:3: note: because ‘SafeVector >’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Main-RNA.cc:894:29: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ In file included from Main-RNA.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = float]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -fdebug-prefix-map=/build/probcons-cynwzx/probcons-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -o pc-makegnuplot MakeGnuPlot.cc -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/probcons-cynwzx/probcons-1.12' make[1]: Leaving directory '/build/probcons-cynwzx/probcons-1.12' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/build/probcons-cynwzx/probcons-1.12' rm -rf /build/probcons-cynwzx/probcons-1.12/debian/probcons-extra/usr/share/doc/probcons-extra dh_link -p probcons-extra usr/share/doc/probcons usr/share/doc/probcons-extra make[1]: Leaving directory '/build/probcons-cynwzx/probcons-1.12' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'probcons' in '../probcons_1.12-13_amd64.deb'. dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-13_amd64.deb'. dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-13_amd64.deb'. dpkg-deb: building package 'probcons-dbgsym' in '../probcons-dbgsym_1.12-13_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../probcons_1.12-13_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/probcons-cynwzx /tmp/probcons-1.12-138rloioqy I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.znflgZBG_x... I: success in 620.0782 seconds md5: probcons-dbgsym_1.12-13_amd64.deb: OK md5: probcons-extra-dbgsym_1.12-13_amd64.deb: OK md5: probcons-extra_1.12-13_amd64.deb: OK md5: probcons_1.12-13_amd64.deb: OK sha1: probcons-dbgsym_1.12-13_amd64.deb: OK sha1: probcons-extra-dbgsym_1.12-13_amd64.deb: OK sha1: probcons-extra_1.12-13_amd64.deb: OK sha1: probcons_1.12-13_amd64.deb: OK sha256: probcons-dbgsym_1.12-13_amd64.deb: OK sha256: probcons-extra-dbgsym_1.12-13_amd64.deb: OK sha256: probcons-extra_1.12-13_amd64.deb: OK sha256: probcons_1.12-13_amd64.deb: OK Checksums: OK