Diff of the two buildlogs: -- --- b1/build.log 2019-06-26 17:10:35.776441564 +0000 +++ b2/build.log 2019-06-26 17:11:23.042234981 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 26 04:59:17 -12 2019 -I: pbuilder-time-stamp: 1561568357 +I: Current time: Wed Jul 29 13:33:37 +14 2020 +I: pbuilder-time-stamp: 1595979217 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Jul 17 07:10:58 2018 -12 +gpgv: Signature made Wed Jul 18 09:10:58 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,6 +31,18 @@ dpkg-source: info: applying fix_pkg-config.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/14111/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14111/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -105,7 +117,7 @@ Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 34 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 35 http://cdn-fastly.deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] -Fetched 19.6 MB in 14s (1367 kB/s) +Fetched 19.6 MB in 1s (30.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -266,9 +278,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (359 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21313 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package libgkarrays dpkg-buildpackage: info: source version 2.1.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -337,7 +381,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-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 a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -370,10 +414,10 @@ checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -392,8 +436,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for ANSI C header files... yes @@ -479,10 +523,10 @@ config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/libProgressBar-1.2.0 (/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0) -configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=i686-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/i386-linux-gnu' '--libexecdir=${prefix}/lib/i386-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=i686-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=. +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/i386-linux-gnu' '--libexecdir=${prefix}/lib/i386-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=i686-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=. 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 a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -502,10 +546,10 @@ checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -525,8 +569,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E @@ -638,7 +682,7 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j10 + make -j18 make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' Making all in src make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' @@ -657,10 +701,10 @@ make all-am make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o testPB.o testPB.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -fPIC -DPIC -o .libs/progressBar.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -o progressBar.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/i386-linux-gnu progressBar.lo +/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/i386-linux-gnu progressBar.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -O6 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libProgressBar.so.0 -o .libs/libProgressBar.so.0.1.2 libtool: link: (cd ".libs" && rm -f "libProgressBar.so.0" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so.0") libtool: link: (cd ".libs" && rm -f "libProgressBar.so" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so") @@ -668,7 +712,7 @@ ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libProgressBar.a libtool: link: ( cd ".libs" && rm -f "libProgressBar.la" && ln -s "../libProgressBar.la" "libProgressBar.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -lProgressBar -Wl,-z,relro -Wl,-z,now -o testProgressBar testPB.o libProgressBar.la +/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -lProgressBar -Wl,-z,relro -Wl,-z,now -o testProgressBar testPB.o libProgressBar.la libtool: link: g++ -O6 -Wall --pedantic --ansi -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testProgressBar testPB.o /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libProgressBar.so make[5]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' @@ -678,24 +722,36 @@ make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buildTables.o buildTables.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArrays.lo gkArrays.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o solArray.lo solArray.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.lo utils.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArraysBuilder.lo gkArraysBuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readsReader.lo readsReader.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o largebinvect.lo largebinvect.cxx +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArrays.lo gkArrays.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o solArray.lo solArray.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.lo utils.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArraysBuilder.lo gkArraysBuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readsReader.lo readsReader.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o largebinvect.lo largebinvect.cxx +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitvector.lo bitvector.cxx +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rank9b.lo `test -f 'sux/rank9b.cpp' || echo './'`sux/rank9b.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -fPIC -DPIC -o .libs/gkIFABuilder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -fPIC -DPIC -o .libs/utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -fPIC -DPIC -o .libs/gkArrays.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -fPIC -DPIC -o .libs/largebinvect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -fPIC -DPIC -o .libs/gkIFABuilder.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.o +sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)': +sux/rank9b.cpp:144:93: warning: suggest parentheses around '-' inside '>>' [-Wparentheses] + return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) ); + ~~~~~~~~~~~~~~~~~~^~~ +sux/rank9b.cpp: In member function 'uint64_t rank9b::select(uint64_t)': +sux/rank9b.cpp:207:81: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] + const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF ); + ~~~~~~~~~~~~~~~~^~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, from buildTables.cpp:111: @@ -708,10 +764,30 @@ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 +gkSABuilder.cpp: In function 'int64_t gkarrays::partition(gkarrays::SolArray*, gkarrays::SolArray*, uintSA, uintSA, uintSA)': +gkSABuilder.cpp:340:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i)))); + ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1 +In file included from readsReader.h:109, + from gkArrays.h:115, + from gkArraysBuilder.h:105, + from gkArraysBuilder.cpp:103: +kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + static int kseq_read(kseq_t *seq) \ + ^~~~~~~~~ +kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + __KSEQ_READ + ^~~~~~~~~~~ +readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' + KSEQ_INIT(gzFile, gzread) + ^~~~~~~~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, - from ./gkIFABuilder.h:107, - from gkIFABuilder.cpp:105: + from ./gkSABuilder.h:108, + from gkSABuilder.cpp:104: +./readsReader.h: At global scope: ./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ @@ -721,22 +797,24 @@ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ -In file included from readsReader.h:109, - from gkArrays.h:115, - from gkCFPSBuilder.cpp:110: -kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1 +In file included from ./readsReader.h:109, + from ./gkArrays.h:115, + from ./gkIFABuilder.h:107, + from gkIFABuilder.cpp:105: +./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ -kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' +./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' __KSEQ_READ ^~~~~~~~~~~ -readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' +./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1 In file included from readsReader.h:109, from gkArrays.h:115, - from gkArraysBuilder.h:105, - from gkArraysBuilder.cpp:103: + from gkCFPSBuilder.cpp:110: kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^~~~~~~~~ @@ -746,10 +824,6 @@ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ -gkSABuilder.cpp: In function 'int64_t gkarrays::partition(gkarrays::SolArray*, gkarrays::SolArray*, uintSA, uintSA, uintSA)': -gkSABuilder.cpp:340:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i)))); - ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from readsReader.h:109, from gkArrays.h:115, from gkArrays.cpp:113: @@ -762,44 +836,14 @@ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ -In file included from ./readsReader.h:109, - from ./gkArrays.h:115, - from ./gkSABuilder.h:108, - from gkSABuilder.cpp:104: -./readsReader.h: At global scope: -./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - static int kseq_read(kseq_t *seq) \ - ^~~~~~~~~ -./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - __KSEQ_READ - ^~~~~~~~~~~ -./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' - KSEQ_INIT(gzFile, gzread) - ^~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitvector.lo bitvector.cxx -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rank9b.lo `test -f 'sux/rank9b.cpp' || echo './'`sux/rank9b.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o -sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)': -sux/rank9b.cpp:144:93: warning: suggest parentheses around '-' inside '>>' [-Wparentheses] - return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) ); - ~~~~~~~~~~~~~~~~~~^~~ -sux/rank9b.cpp: In member function 'uint64_t rank9b::select(uint64_t)': -sux/rank9b.cpp:207:81: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] - const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF ); - ~~~~~~~~~~~~~~~~^~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -o gkCFPSBuilder.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -o readsReader.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -o gkCFPSBuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -o gkIFABuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -Wl,-rpath -Wl,/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so -lpthread -lz -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: link: (cd ".libs" && rm -f "libGkArrays.so.1" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so.1") libtool: link: (cd ".libs" && rm -f "libGkArrays.so" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so") @@ -807,7 +851,7 @@ ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libGkArrays.a libtool: link: ( cd ".libs" && rm -f "libGkArrays.la" && ln -s "../libGkArrays.la" "libGkArrays.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/buildTables buildTables.o /build/libgkarrays-2.1.0+dfsg/src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libGkArrays.so -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' @@ -820,7 +864,7 @@ make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' dh_auto_test - make -j10 check VERBOSE=1 + make -j18 check VERBOSE=1 make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' Making check in src make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' @@ -891,13 +935,13 @@ /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testPairedEnd testPairedEnd.o checkPairedEnd.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testVariableFixed testVariableFixed.o compareVariableFixed.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testVariableFixed testVariableFixed.o compareVariableFixed.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testConsistency testConsistency.o checkConsistency.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make check-TESTS @@ -938,7 +982,7 @@ make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq' /usr/bin/install -c -m 644 kseq.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' @@ -946,7 +990,7 @@ make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux' /usr/bin/install -c -m 644 macros.h popcount.h rank9b.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' @@ -955,8 +999,8 @@ Making install in libProgressBar make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar.so.0.1.2 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so.0 || { rm -f libProgressBar.so.0 && ln -s libProgressBar.so.0.1.2 libProgressBar.so.0; }; }) libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so || { rm -f libProgressBar.so && ln -s libProgressBar.so.0.1.2 libProgressBar.so; }; }) @@ -965,9 +1009,9 @@ libtool: install: chmod 644 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar.a libtool: install: ranlib /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar-1.2.0/include' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar-1.2.0/include' /usr/bin/install -c -m 644 config.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar-1.2.0/include' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0' /usr/bin/install -c -m 644 progressBar.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0' make install-data-hook make[6]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' @@ -978,7 +1022,7 @@ make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[5]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libProgressBar-1.2.0.pc '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' make install-data-hook make[6]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' @@ -989,10 +1033,10 @@ make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: warning: relinking 'libGkArrays.la' -libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/src; /bin/bash "/build/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/libgkarrays-2.1.0+dfsg/debian/tmp) +libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/src; /bin/sh "/build/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/libgkarrays-2.1.0+dfsg/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: install: /usr/bin/install -c .libs/libGkArrays.so.1.1.0T /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays.so.1.1.0 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so.1 || { rm -f libGkArrays.so.1 && ln -s libGkArrays.so.1.1.0 libGkArrays.so.1; }; }) @@ -1002,9 +1046,9 @@ libtool: install: chmod 644 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays.a libtool: install: ranlib /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0' /usr/bin/install -c -m 644 gkArrays.h solArray.h gkArraysTypes.h gkArraysBuilder.h gkSABuilder.h gkCFPSBuilder.h gkIFABuilder.h readsReader.h bitvector.hxx largebinvect.hxx bitvector.cxx largebinvect.cxx binvect.hxx '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0' - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays-2.1.0/include' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays-2.1.0/include' /usr/bin/install -c -m 644 /build/libgkarrays-2.1.0+dfsg/config/config.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays-2.1.0/include' make install-data-hook make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' @@ -1023,7 +1067,7 @@ make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' + /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libGkArrays-2.1.0.pc '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' make install-data-hook make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg' @@ -1081,8 +1125,8 @@ dpkg-gencontrol: warning: package libgkarrays-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libgkarrays1' in '../libgkarrays1_2.1.0+dfsg-2_i386.deb'. dpkg-deb: building package 'libgkarrays1-dbgsym' in '../libgkarrays1-dbgsym_2.1.0+dfsg-2_i386.deb'. +dpkg-deb: building package 'libgkarrays1' in '../libgkarrays1_2.1.0+dfsg-2_i386.deb'. dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libgkarrays_2.1.0+dfsg-2_i386.changes @@ -1090,12 +1134,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/14111/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14111/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/24015 and its subdirectories -I: Current time: Wed Jun 26 05:10:35 -12 2019 -I: pbuilder-time-stamp: 1561569035 +I: removing directory /srv/workspace/pbuilder/14111 and its subdirectories +I: Current time: Wed Jul 29 13:34:23 +14 2020 +I: pbuilder-time-stamp: 1595979263