Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/codonw/codonw_1.4.4-6_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/codonw-1.4.4-6tfhhd60h/codonw_1.4.4-6_amd64.buildinfo Get source package info: codonw=1.4.4-6 Source URL: http://snapshot.notset.fr/mr/package/codonw/1.4.4-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid1=2.36.1-7 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.1-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdpkg-perl=1.20.7.1 libelf1=0.183-1 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-4 libpam-modules-bin=1.4.0-4 libpam-runtime=1.4.0-4 libpam0g=1.4.0-4 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-2 libpipeline1=1.5.3-1 libquadmath0=10.2.1-6 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.36.1-7 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-1 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.13-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-2 perl-base=5.32.1-2 perl-modules-5.32=5.32.1-2 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.34+dfsg-1 util-linux=2.36.1-7 xz-utils=5.2.5-1.0 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/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ 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 codonw=1.4.4-6 && mkdir -p /build/codonw-20wuW3 && dpkg-source --no-check -x /*.dsc /build/codonw-20wuW3/codonw-1.4.4 && chown -R builduser:builduser /build/codonw-20wuW3" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/codonw-20wuW3/codonw-1.4.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613813076" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/codonw-20wuW3 /tmp/codonw-1.4.4-6tfhhd60h bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210218T111050Z 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.lPEiwLrFeB 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.lPEiwLrFeB Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). 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/20210218T111050Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1106 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 ... 4662 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210218T111050Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.lPEiwLrFeB Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210218T111050Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages [11.9 MB] Fetched 34.6 MB in 30s (1172 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.lPEiwLrFeB I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d codonw=1.4.4-6 && mkdir -p /build/codonw-20wuW3 && dpkg-source --no-check -x /*.dsc /build/codonw-20wuW3/codonw-1.4.4 && chown -R builduser:builduser /build/codonw-20wuW3"' exec /tmp/mmdebstrap.lPEiwLrFeB Reading package lists... NOTICE: 'codonw' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/codonw.git Please use: git clone https://salsa.debian.org/med-team/codonw.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 170 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main codonw 1.4.4-6 (dsc) [1913 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main codonw 1.4.4-6 (tar) [156 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main codonw 1.4.4-6 (diff) [12.1 kB] Fetched 170 kB in 0s (1034 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'codonw_1.4.4-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting codonw in /build/codonw-20wuW3/codonw-1.4.4 dpkg-source: info: unpacking codonw_1.4.4.orig.tar.gz dpkg-source: info: unpacking codonw_1.4.4-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying enable_clean dpkg-source: info: applying remove_pause dpkg-source: info: applying define_linux dpkg-source: info: applying spelling dpkg-source: info: applying helpfile_location dpkg-source: info: applying fix_link_name_clashes dpkg-source: info: applying remove_nondeterminism I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/codonw-20wuW3/codonw-1.4.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1613813076" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.lPEiwLrFeB dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' rm -rf *.o *.coa *.blk *.out *raw codonw codonW.log make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' debian/rules override_dh_clean make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' rm -rf debian/man dh_clean --exclude=Makefile.orig make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codons.c cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.c cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 commline.c In file included from codon_us.c:77: codon_us.c: In function ‘codon_error’: codonW.h:38:74: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} | ^~~~ codon_us.c:347:6: note: in expansion of macro ‘pause’ 347 | pause; | ^~~~~ codon_us.c: In function ‘codon_usage_out’: codon_us.c:373:24: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 373 | fprintf(fblkout, "%i%c",nncod[x],sp); | ~^ ~~~~~~~~ | | | | int long int | %li In file included from commline.c:28: commline.c: In function ‘proc_comm_line’: codonW.h:38:74: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} | ^~~~ commline.c:103:2: note: in expansion of macro ‘pause’ 103 | pause; | ^~~~~ codon_us.c: In function ‘raau_usage_out’: codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] 479 | fprintf(fblkout, "\n",sp); | ^~~~ codon_us.c: In function ‘cbi_out’: codon_us.c:831:32: warning: format ‘%f’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] 831 | sprintf(pm->messages, " Serious error in CBI information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 836 | pcbi->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codon_us.c:832:38: note: format string is defined here 832 | " an illegal CBI value of %f for codon %i" | ~^ | | | double | %d codon_us.c: In function ‘fop_out’: codon_us.c:988:28: warning: format ‘%f’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 993 | pfop->fop_cod[x], x); | ~~~~~~~~~~~~~~~~ | | | int codon_us.c:989:37: note: format string is defined here 989 | " an illegal fop value of %f for codon %l" | ~^ | | | double | %d codon_us.c:988:28: warning: unknown conversion type character ‘ ’ in format [-Wformat=] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:990:11: note: format string is defined here 990 | " permissible values are \n 1 for non-optimal" | ^ codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:994:18: warning: unknown conversion type character ‘,’ in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:26: warning: unknown conversion type character ‘,’ in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^ codon_us.c:994:37: warning: unknown conversion type character ‘\x0a’ in format [-Wformat=] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~ codon_us.c:994:11: warning: too many arguments for format [-Wformat-extra-args] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function ‘gc_out’: codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args] 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ open_fil.c: In function ‘open_file’: open_fil.c:88:13: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 88 | gets(infile_name); /* get filename */ | ^~~~ | fgets codons.c: In function ‘main’: codons.c:190:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", | ~^ | | | int | %li 191 | num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:196:25: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 | " input file has\ninternal stop codons (found %i" 198 | " internal stops) \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int codons.c:197:68: note: format string is defined here 197 | " input file has\ninternal stop codons (found %i" | ~^ | | | int | %li codons.c:200:39: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " | ~^ | | | int | %li 201 | "stop codons \tWARNING\n",num_seq_int_stop); | ~~~~~~~~~~~~~~~~ | | | long int open_fil.c:128:28: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 128 | fprintf(stderr,"\nThese are the files in the current directory " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); | ~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} codon_us.c: In function ‘dinuc_out’: open_fil.c:129:34: note: format string is defined here 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); | ~~^~ | | | int codon_us.c:1476:32: warning: precision used with ‘%c’ gnu_printf format [-Wformat=] 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); | ^ In file included from codons.c:90: codonW.h:38:74: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} | ^~~~ codons.c:204:35: note: in expansion of macro ‘pause’ 204 | if ( pm->codonW && pm->menu ) pause; | ^~~~~ open_fil.c:162:52: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 162 | fprintf(stderr, "\nWarning :File %.*s " | ~~^~ | | | int ...... 165 | strlen(infile_name), infile_name); | ~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} open_fil.c:166:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 166 | fgets(temp, 3, stdin); | ^~~~~~~~~~~~~~~~~~~~~ codons.c: In function ‘toutput’: codons.c:640:25: warning: unknown conversion type character ‘=’ in format [-Wformat=] 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:641:11: note: format string is defined here 641 | " =%5.3f\n" /* with G+C content and length of gene */ | ^ codons.c:647:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ~^ | | | int | %ld 648 | "in sequence %i\n" 649 | ,non_std_char - IUBC_TOT | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long int codons.c:647:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 650 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:648:25: note: format string is defined here 648 | "in sequence %i\n" | ~^ | | | int | %li codons.c:652:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" | ~~^ | | | int | %3li 653 | ,num_sequence | ~~~~~~~~~~~~ | | | long int codons.c:657:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ~^ | | | int | %ld ...... 660 | ,non_std_char | ~~~~~~~~~~~~ | | | long int codon_us.c: In function ‘hydro_out’: codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args] 2115 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: In function ‘aromo_out’: codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args] 2148 | fprintf(pm->my_err, "No output was written to file \n", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:657:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 657 | fprintf(pm->my_err, "\t\t WARNING %d non " | ^~~~~~~~~~~~~~~~~~~~~~ ...... 661 | ,num_sequence); | ~~~~~~~~~~~~ | | | long int codons.c:659:25: note: format string is defined here 659 | "in sequence %i\n" | ~^ | | | int | %li codons.c: In function ‘output’: codons.c:800:34: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=] 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codons.c:805:32: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=] 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); | ~^ ~~~~~~~~ | | | | char * int | %d codon_us.c: In function ‘gen_cusort_fop’: codon_us.c:1699:8: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1700:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1703:8: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ | ^~~~~~~~~~~~~~~~~~~~~~~ codon_us.c:1711:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.c In file included from menu.c:31: menu.c: In function ‘main_menu’: codonW.h:38:74: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} | ^~~~ menu.c:69:9: note: in expansion of macro ‘pause’ 69 | pause; | ^~~~~ In file included from /usr/include/stdio.h:867, from commline.c:26: In function ‘printf’, inlined from ‘proc_comm_line’ at commline.c:620:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:107:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 107 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function ‘printinfo’: menu.c:1285:26: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1285 | printf("\tVersion : %.*s\n", strlen(Revision) , Revision ); | ~~^~ ~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.c tester.c: In function ‘tester’: tester.c:88:17: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] 88 | gets( pm->junk ) ; | ^~~~ | fgets cc -c -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c coresp.c: In function ‘textbin’: coresp.c:98:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pm->fcoa_in,"%s",pm->junk); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:104:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:108:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:115:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:119:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fscanf(pm->fcoa_in,"%i\n",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:127:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | fscanf(pm->fcoa_in,"%i",&v2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:131:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function ‘rowout’: coresp.c:277:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 277 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function ‘inertialig’: coresp.c:1271:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1271 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c:1315:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1315 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ coresp.c: In function ‘suprow’: coresp.c:1619:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1619 | fgets(pm->junk,BUFSIZ,fnam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/codonw-20wuW3/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wl,-z,relro -Wl,-z,now codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o -o codonw -lm /usr/bin/ld: codon_us.o: in function `cai_out': ./codon_us.c:652: warning: the `gets' function is dangerous and should not be used. make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' mkdir -p debian/codonw/usr/bin cp codonw debian/codonw/usr/bin mkdir -p debian/codonw/usr/share/codonw cp codonW.hlp debian/codonw/usr/share/codonw chmod -x debian/codonw/usr/share/codonw/codonW.hlp make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' dh_install -a debian/rules override_dh_installdocs make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' mkdir -p debian/codonw/usr/share/doc/codonw cp *.txt debian/codonw/usr/share/doc/codonw mkdir -p debian/codonw/usr/share/doc-base cp debian/doc-base debian/codonw/usr/share/doc-base/codonw-doc dh_installdocs -- make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' mkdir -p /build/codonw-20wuW3/codonw-1.4.4/debian/man /build/codonw-20wuW3/codonw-1.4.4/debian/make_man.pl /build/codonw-20wuW3/codonw-1.4.4/debian/template.man \ /build/codonw-20wuW3/codonw-1.4.4/debian/man calculate Amino Acid Usage (AAU) silent base G+C+A+T calculating program calculate Effective Number of Codons (ENc) tabulation of codon usage calculate codon usage calculate Codon Bias Index (CBI) G+C content of gene (all 3 codon positions) conceptual translation of DNA to amino acid calculate Relative Synonymous Codon Usage (RSCU) dinucleotide usage of the three codon positions detailed report of base composition clean up sequence in FASTA format GC of synonymous codons 3rd positions calculate Codon Adaptation Index (CAI) calculate Frequency of OPtimal codons index (FOP) tabulation of datasets codon usage calculate Relative Amino Acid Usage (RAAU) output sequence in reader format dh_installman -- make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/codonw-20wuW3/codonw-1.4.4' dh_fixperms chmod -x debian/codonw/usr/share/doc/codonw/examples/input.dat make[1]: Leaving directory '/build/codonw-20wuW3/codonw-1.4.4' 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 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-6_amd64.deb'. dpkg-deb: building package 'codonw' in '../codonw_1.4.4-6_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../codonw_1.4.4-6_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/codonw-20wuW3 /tmp/codonw-1.4.4-6tfhhd60h I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.lPEiwLrFeB... I: success in 277.6561 seconds md5: codonw-dbgsym_1.4.4-6_amd64.deb: OK md5: codonw_1.4.4-6_amd64.deb: OK sha1: codonw-dbgsym_1.4.4-6_amd64.deb: OK sha1: codonw_1.4.4-6_amd64.deb: OK sha256: codonw-dbgsym_1.4.4-6_amd64.deb: OK sha256: codonw_1.4.4-6_amd64.deb: OK Checksums: OK