Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/maq/maq_0.7.1-9_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/maq-0.7.1-9my921tz2/maq_0.7.1-9_amd64.buildinfo Get source package info: maq=0.7.1-9 Source URL: http://snapshot.notset.fr/mr/package/maq/0.7.1-9/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=2.36-4 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 zlib1g-dev=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/20201116T150139Z/ unstable 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 maq=0.7.1-9 && mkdir -p /build/maq-FOGpzv && dpkg-source --no-check -x /*.dsc /build/maq-FOGpzv/maq-0.7.1 && chown -R builduser:builduser /build/maq-FOGpzv" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/maq-FOGpzv/maq-0.7.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605521780" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/maq-FOGpzv /tmp/maq-0.7.1-9my921tz2 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.dtT3hGeim6 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.dtT3hGeim6 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 (926 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/20201116T150139Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.dtT3hGeim6 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201116T092020Z 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/20201116T150139Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201116T150139Z unstable/main amd64 Packages [11.5 MB] Fetched 34.3 MB in 28s (1206 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.dtT3hGeim6 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d maq=0.7.1-9 && mkdir -p /build/maq-FOGpzv && dpkg-source --no-check -x /*.dsc /build/maq-FOGpzv/maq-0.7.1 && chown -R builduser:builduser /build/maq-FOGpzv"' exec /tmp/mmdebstrap.dtT3hGeim6 Reading package lists... NOTICE: 'maq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/maq.git Please use: git clone https://salsa.debian.org/med-team/maq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 412 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main maq 0.7.1-9 (dsc) [1948 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main maq 0.7.1-9 (tar) [398 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main maq 0.7.1-9 (diff) [11.4 kB] Fetched 412 kB in 1s (814 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'maq_0.7.1-9.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting maq in /build/maq-FOGpzv/maq-0.7.1 dpkg-source: info: unpacking maq_0.7.1.orig.tar.gz dpkg-source: info: unpacking maq_0.7.1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_prevent_-64_option.patch dpkg-source: info: applying gcc-4.7.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/maq-FOGpzv/maq-0.7.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605521780" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.dtT3hGeim6 dpkg-buildpackage: info: source package maq dpkg-buildpackage: info: source version 0.7.1-9 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_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:6: installing './compile' dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h dh_auto_build -a make -j4 make[1]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' make all-am make[2]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o const.o const.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.o seq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bfa.o bfa.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o read.o read.cc bfa.c: In function ‘nst_load_bfa1’: bfa.c:31:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 31 | fread(bfa1->name, sizeof(char), len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:32:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:33:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | fread(&bfa1->len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:35:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:37:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c: In function ‘nst_bfa_len’: bfa.c:46:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 46 | fread(&len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:48:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 48 | fread(&len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta2bfa.o fasta2bfa.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastq2bfq.o fastq2bfq.c fastq2bfq.c: In function ‘fastq2bfq’: fastq2bfq.c:30:5: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 30 | fp = gzopen(str, "w"); | ^ fastq2bfq.c:36:7: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 36 | fp = gzopen(str, "w"); | ^ fastq2bfq.c:47:11: warning: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] 47 | gzwrite(fp, &i, sizeof(int)); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ fastq2bfq.c:48:11: warning: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] 48 | gzwrite(fp, name, sizeof(char) * i); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ fastq2bfq.c:49:11: warning: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] 49 | gzwrite(fp, &l, sizeof(int)); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ fastq2bfq.c:50:11: warning: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] 50 | gzwrite(fp, seq.s, sizeof(char) * l); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ fastq2bfq.c:53:12: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 53 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ fastq2bfq.c:62:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 62 | gzclose(fp); | ^~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o merge.o merge.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match.o match.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc sort_mapping.cc: In function ‘int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)’: sort_mapping.cc:59:61: warning: suggest parentheses around arithmetic in operand of ‘^’ [-Wparentheses] 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); | ~~~~~~^~~~~~~~~ match.cc: In function ‘int alt_cal_mm(bit64_t)’: match.cc:58:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; | ~~^~~~~~~~~~ match.cc:61:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 61 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ match.cc: In function ‘int alt_cal_err(bit64_t, bit64_t)’: match.cc:67:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 67 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; | ~~^~~~~~~~~~ match.cc:70:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 70 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ match.cc: In function ‘void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)’: match.cc:284:39: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ref_canlist_t’; use assignment or value-initialization instead [-Wclass-memaccess] 284 | memset(list, 0, sizeof(ref_canlist_t)); | ^ match.cc:49:16: note: ‘struct ref_canlist_t’ declared here 49 | typedef struct { | ^ match.cc: In function ‘void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)’: match.cc:292:10: warning: variable ‘n_reads’ set but not used [-Wunused-but-set-variable] 292 | bit32_t n_reads; | ^~~~~~~ match.cc: In function ‘int ma_match(int, char**)’: match.cc:525:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fscanf(tmpfp, "%s", adaptor); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.cc assemble.cc: In function ‘base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)’: assemble.cc:106:63: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; | ~~~~^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_pos.o get_pos.c mapcheck.cc: In function ‘int ma_mapcheck(int, char**)’: mapcheck.cc:60:17: warning: variable ‘fpout’ set but not used [-Wunused-but-set-variable] 60 | FILE *fp_bfa, *fpout; | ^~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc rbcc.cc: In function ‘hash_map_char* cns_load_dbSNP(FILE*)’: rbcc.cc:21:21: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 21 | sprintf(str1, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:867, from rbcc.cc:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc indel_soa.cc: In function ‘void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)’: indel_soa.cc:42:40: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses] 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ indel_soa.cc:56:40: warning: suggest parentheses around ‘-’ inside ‘<<’ [-Wparentheses] 56 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap.o maqmap.c subsnp.cc: In function ‘hash_map_char* ma_load_snp(FILE*)’: subsnp.cc:20:20: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 20 | sprintf(key, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:867, from subsnp.cc:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subsnp.cc: In function ‘hash_set_char* ma_load_snp_set(FILE*)’: subsnp.cc:35:20: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 35 | sprintf(key, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:867, from subsnp.cc:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o submap.o submap.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc subsnp.cc: In function ‘void maq_simucns_core(FILE*, gzFile, FILE*)’: subsnp.cc:190:21: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 190 | sprintf(key, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:867, from subsnp.cc:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subsnp.cc:186:22: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 186 | sprintf(key, "%s.%d", name, i); | ^~ In file included from /usr/include/stdio.h:867, from subsnp.cc:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 3 and 268 bytes into a destination of size 256 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c simulate.c: In function ‘maq_simutrain’: simulate.c:83:8: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] 83 | fpout = gzopen(argv[1], "w"); | ^ simulate.c:86:10: warning: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] 86 | gzwrite(fpout, fqc, sizeof(fqc_t)); | ^~~~~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from simulate.c:6: /usr/include/zlib.h:1446:29: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1446 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, | ^~ simulate.c:87:10: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] 87 | gzclose(fpout); | ^~~~~ | | | struct gzFile_s ** In file included from /usr/include/zlib.h:34, from simulate.c:6: /usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’ 1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o genran.o genran.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc In file included from /usr/include/string.h:495, from maqmap.h:23, from simulate.c:11: In function ‘memset’, inlined from ‘simustat_core’ at simulate.c:386:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:71:10: warning: ‘__builtin___memset_chk’ offset [16, 31] is out of the bounds [0, 16] of object ‘tc’ with type ‘int[2][2]’ [-Warray-bounds] 71 | return __builtin___memset_chk (__dest, __ch, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simulate.c: In function ‘simustat_core’: simulate.c:381:12: note: ‘tc’ declared here 381 | int i, k, tc[2][2]; | ^~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.c stdaln.c: In function ‘aln_local_core’: stdaln.c:534:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 534 | int gap_open, gap_ext, b; | ^ In file included from /usr/include/string.h:495, from rmdup.cc:2: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:46:11, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:39:21, inlined from ‘void maq_rmdup_core(gzFile, gzFile)’ at rmdup.cc:102:23: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rmdup.cc: In function ‘void maq_rmdup_core(gzFile, gzFile)’: rmdup.cc:42:26: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ In file included from /usr/include/string.h:495, from rmdup.cc:2: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:46:11, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:39:21, inlined from ‘void maq_rmdup_core(gzFile, gzFile)’ at rmdup.cc:94:37: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rmdup.cc: In function ‘void maq_rmdup_core(gzFile, gzFile)’: rmdup.cc:42:26: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ In file included from /usr/include/string.h:495, from rmdup.cc:2: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:46:11, inlined from ‘char* trim_name(char*, char*)’ at rmdup.cc:39:21, inlined from ‘void maq_rmdup_core(gzFile, gzFile)’ at rmdup.cc:92:31: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rmdup.cc: In function ‘void maq_rmdup_core(gzFile, gzFile)’: rmdup.cc:42:26: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc eland2maq.cc: In function ‘void eland2maq_core(FILE*, FILE*, gzFile)’: eland2maq.cc:88:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fscanf(fp_eland, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:96:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(fp_eland, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:99:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(fp_eland, "%u%u%u%s%u%s", tmp, tmp+1, tmp+2, str, tmp+3, str2); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eland2maq.cc: In function ‘hash_map_char* read_list(FILE*)’: eland2maq.cc:33:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | fscanf(fp, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~ eland2maq.cc: In function ‘void novo2maq_core(FILE*, FILE*, gzFile)’: eland2maq.cc:323:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 323 | fgets( str2, 4096, fp_novo ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c In file included from break_pair.c:2: break_pair.c: In function ‘breakpair’: break_pair.c:16:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 16 | assert(fp = gzopen(str, "r")); | ^~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc glfgen.cc: In function ‘glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)’: glfgen.cc:43:63: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 43 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; | ~~~~^~~~~~~~~ eland2maq.cc: In function ‘void export2maq_core(FILE*, FILE*, gzFile)’: eland2maq.cc:563:21: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 563 | sprintf(str2, "%s_%d:%d:%d:%d:%d", str, ti[0], ti[1], ti[2], ti[3], ti[4]); | ^~ In file included from /usr/include/stdio.h:867, from eland2maq.cc:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 11 and 1084 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -fdebug-prefix-map=/build/maq-FOGpzv/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz make[2]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' make[1]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' make[1]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/build/maq-FOGpzv/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' make[2]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/maq-FOGpzv/maq-0.7.1/debian/maq/usr/bin' /bin/mkdir -p '/build/maq-FOGpzv/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/maq-FOGpzv/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/maq-FOGpzv/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' make[1]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' dh_installman # when installing via debian/manpages the .pl is stripped and the # files will end up in /usr/share/man/pl/man1 cp -a debian/mans/*.1 debian/maq/usr/share/man/man1 make[1]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/build/maq-FOGpzv/maq-0.7.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/maq-FOGpzv/maq-0.7.1' 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 dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_amd64.deb'. dpkg-deb: building package 'maq' in '../maq_0.7.1-9_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../maq_0.7.1-9_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/maq-FOGpzv /tmp/maq-0.7.1-9my921tz2 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.dtT3hGeim6... I: success in 557.9117 seconds md5: maq-dbgsym_0.7.1-9_amd64.deb: OK md5: maq_0.7.1-9_amd64.deb: OK sha1: maq-dbgsym_0.7.1-9_amd64.deb: OK sha1: maq_0.7.1-9_amd64.deb: OK sha256: maq-dbgsym_0.7.1-9_amd64.deb: OK sha256: maq_0.7.1-9_amd64.deb: OK Checksums: OK