Hi Steffen, > Please someone help me out. Pizzly is lintian clean when built > "regularly" on my desktop but fails with > > /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8a4be.dir/link.txt > --verbose=1 > /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/pizzly-0.37.3=. > -fstack-protector-strong -Wformat -Werror=format-security -Wall > -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 > -DCHECK_FUNCTION_EXISTS=pthread_create -Wl,-z,relro -Wl,-z,now > -Wl,--as-needed -rdynamic > CMakeFiles/cmTC_8a4be.dir/CheckFunctionExists.cxx.o -o cmTC_8a4be > -lpthreads > /usr/bin/ld: cannot find -lpthreads > > in pbuilder. Interesting. I get a different problem when building in a recent unstable chroot (there's a long list of unrelated debug stuff after the original root cause message): $ gbp buildpackage -uc -us --git-pbuilder --git-pristine-tar --git-ignore-new gbp:info: Building with (cowbuilder) for unstable Building with cowbuilder for distribution unstable [...] dh build dh_update_autotools_config dh_autoreconf dh_auto_configure install -d obj-x86_64-linux-gnu cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 8.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR) -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: ZLIB_LIBRARY linked by target "pizzly" in directory /build/pizzly-0.37.3 After simply adding a build-dep to zlib1g-dev, everything built fine for me. See the attached build log. Cheers Sascha
gbp:info: Building with (cowbuilder) for unstable Building with cowbuilder for distribution unstable [0mI: using cowbuilder as pbuilder[0m dpkg-checkbuilddeps: error: Unmet build dependencies: libseqan2-dev cmake [1;33mW: Unmet build-dependency in source[0m dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/home/satta/pkg/deb-med/pizzly' dh_auto_clean rm -f debian/pizzly.1 make[1]: Leaving directory '/home/satta/pkg/deb-med/pizzly' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pizzly.substvars debian/files rm -fr -- debian/pizzly/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building pizzly using existing ./pizzly_0.37.3.orig.tar.xz dpkg-source: info: building pizzly in pizzly_0.37.3-1.debian.tar.xz dpkg-source: info: building pizzly in pizzly_0.37.3-1.dsc [0mI: Generated dsc will be overwritten by build result; not generating changes file[0m [0mI: Copying COW directory[0m [0mI: forking: rm -rf /var/cache/pbuilder/build/cow.22563[0m [0mI: forking: cp -al /var/cache/pbuilder/base-unstable.cow /var/cache/pbuilder/build/cow.22563[0m [0mI: removed stale ilistfile /var/cache/pbuilder/build/cow.22563/.ilist[0m [0mI: forking: chroot /var/cache/pbuilder/build/cow.22563 cowdancer-ilistcreate /.ilist 'find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a -links +1 -print0 \) | xargs -0 stat --format '%d %i ''[0m [0mI: Invoking pbuilder[0m [0mI: forking: pbuilder build --debbuildopts --debbuildopts ' '-uc' '-us'' --buildplace /var/cache/pbuilder/build/cow.22563 --buildresult /home/satta/pkg/deb-med --mirror http://ftp.us.debian.org/debian/ --distribution unstable --extrapackages 'debhelper fakeroot apt-utils' --no-targz --internal-chrootexec 'chroot /var/cache/pbuilder/build/cow.22563 cow-shell' /home/satta/pkg/deb-med/pizzly_0.37.3-1.dsc[0m [0mI: Running in no-targz mode[0m [1;33mW: pbuilder: network will not be disabled during build![0m [0mI: Current time: Tue Jun 4 12:26:22 CEST 2019[0m [0mI: pbuilder-time-stamp: 1559643982[0m [0mI: copying local configuration[0m [1;33mW: hookdir /home/satta/.pbuilder/build-hooks does not exist, skipping[0m [1;33mW: --override-config is not set; not updating apt.conf Read the manpage for details.[0m [0mI: mounting /proc filesystem[0m [0mI: mounting /sys filesystem[0m [0mI: creating /{dev,run}/shm[0m [0mI: mounting /dev/pts filesystem[0m [0mI: redirecting /dev/ptmx to /dev/pts/ptmx[0m [0mI: Mounting /dev/shm[0m [0mI: Mounting /home/satta/_pbuilder_local_deps[0m [0mI: Mounting /var/cache/pbuilder/ccache[0m [0mI: policy-rc.d already exists[0m [0mI: Obtaining the cached apt archive contents[0m [0mI: Copying source file[0m [0mI: copying [/home/satta/pkg/deb-med/pizzly_0.37.3-1.dsc][0m [0mI: copying [/home/satta/pkg/deb-med/pizzly_0.37.3.orig.tar.xz][0m [0mI: copying [/home/satta/pkg/deb-med/pizzly_0.37.3-1.debian.tar.xz][0m [0mI: Extracting source[0m dpkg-source: warning: extracting unsigned source package (pizzly_0.37.3-1.dsc) dpkg-source: info: extracting pizzly in pizzly-0.37.3 dpkg-source: info: unpacking pizzly_0.37.3.orig.tar.xz dpkg-source: info: unpacking pizzly_0.37.3-1.debian.tar.xz [0mI: using fakeroot in build.[0m [0mI: Installing the build-deps[0m -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org> Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), libseqan2-dev, help2man, cmake, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18126 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: cmake{a} cmake-data{a} help2man{a} libarchive13{a} libcurl4{a} libexpat1{a} libgssapi-krb5-2{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libnghttp2-14{a} libprocps7{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1{a} libssl1.1{a} libuv1{a} lsb-base{a} procps{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates krb5-locales libsasl2-modules psmisc publicsuffix 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/11.1 MB of archives. After unpacking 51.2 MB will be used. Writing extended state information... Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-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 ... 18126 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../01-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../02-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../04-cmake-data_3.13.4-1_all.deb ... Unpacking cmake-data (3.13.4-1) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../05-libarchive13_3.3.3-4_amd64.deb ... Unpacking libarchive13:amd64 (3.3.3-4) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../07-libkrb5support0_1.17-2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../08-libk5crypto3_1.17-2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-2) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../09-libssl1.1_1.1.1c-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1c-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../10-libkrb5-3_1.17-2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-2) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../11-libgssapi-krb5-2_1.17-2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../12-libsasl2-modules-db_2.1.27+dfsg-1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../13-libsasl2-2_2.1.27+dfsg-1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../14-libldap-common_2.4.47+dfsg-3_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../15-libldap-2.4-2_2.4.47+dfsg-3_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../16-libnghttp2-14_1.37.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.37.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../17-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../18-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../19-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../20-libcurl4_7.64.0-3_amd64.deb ... Unpacking libcurl4:amd64 (7.64.0-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../21-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../22-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../23-librhash0_1.3.8-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.8-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../24-libuv1_1.24.1-1_amd64.deb ... Unpacking libuv1:amd64 (1.24.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../25-cmake_3.13.4-1_amd64.deb ... Unpacking cmake (3.13.4-1) ... Selecting previously unselected package help2man. Preparing to unpack .../26-help2man_1.47.10_amd64.deb ... Unpacking help2man (1.47.10) ... Selecting previously unselected package libseqan2-dev. Preparing to unpack .../27-libseqan2-dev_2.4.0+dfsg-11_all.deb ... Unpacking libseqan2-dev (2.4.0+dfsg-11) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../28-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up libexpat1:amd64 (2.2.6-1) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libarchive13:amd64 (3.3.3-4) ... Setting up libssl1.1:amd64 (1.1.1c-1) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libnghttp2-14:amd64 (1.37.0-1) ... Setting up libldap-common (2.4.47+dfsg-3) ... Setting up libkrb5support0:amd64 (1.17-2) ... Setting up libseqan2-dev (2.4.0+dfsg-11) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Setting up libuv1:amd64 (1.24.1-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libk5crypto3:amd64 (1.17-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up librhash0:amd64 (1.3.8-1) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:amd64 (1.17-2) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3) ... Setting up help2man (1.47.10) ... Setting up libgssapi-krb5-2:amd64 (1.17-2) ... Setting up libcurl4:amd64 (7.64.0-3) ... Setting up cmake (3.13.4-1) ... Processing triggers for man-db (2.8.5-2) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... apt-utils is already the newest version (1.8.2). debhelper is already the newest version (12.1.1). fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. [0mI: Copying back the cached apt archive contents[0m [0mI: Building the package[0m [0mI: Running cd /build/pizzly-0.37.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc '-uc' '-us'[0m dpkg-buildpackage: info: source package pizzly dpkg-buildpackage: info: source version 0.37.3-1 dpkg-buildpackage: info: source distribution UNRELEASED dpkg-buildpackage: info: source changed by Steffen Moeller <moeller@debian.org> dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pizzly-0.37.3' dh_auto_clean rm -f debian/pizzly.1 make[1]: Leaving directory '/build/pizzly-0.37.3' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pizzly.substvars debian/files rm -fr -- debian/pizzly/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) dpkg-source -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building pizzly using existing ./pizzly_0.37.3.orig.tar.xz dpkg-source: info: building pizzly in pizzly_0.37.3-1.debian.tar.xz dpkg-source: info: building pizzly in pizzly_0.37.3-1.dsc debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure install -d obj-x86_64-linux-gnu cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 8.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/pizzly-0.37.3/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j6 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/pizzly-0.37.3 -B/build/pizzly-0.37.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/pizzly-0.37.3/obj-x86_64-linux-gnu/CMakeFiles /build/pizzly-0.37.3/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/depend make[3]: Entering directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' cd /build/pizzly-0.37.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/pizzly-0.37.3 /build/pizzly-0.37.3 /build/pizzly-0.37.3/obj-x86_64-linux-gnu /build/pizzly-0.37.3/obj-x86_64-linux-gnu /build/pizzly-0.37.3/obj-x86_64-linux-gnu/CMakeFiles/pizzly.dir/DependInfo.cmake --color= Scanning dependencies of target pizzly make[3]: Leaving directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/build make[3]: Entering directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' [ 50%] Building CXX object CMakeFiles/pizzly.dir/main.cpp.o /usr/bin/c++ -I/build/pizzly-0.37.3/. -g -O2 -fdebug-prefix-map=/build/pizzly-0.37.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -DSEQAN_HAS_ZLIB=1 -o CMakeFiles/pizzly.dir/main.cpp.o -c /build/pizzly-0.37.3/main.cpp In file included from /build/pizzly-0.37.3/main.cpp:6: /build/pizzly-0.37.3/common.h: In constructor 'ProgramOptions::ProgramOptions()': /build/pizzly-0.37.3/common.h:18:7: warning: 'ProgramOptions::kmerScore' will be initialized after [-Wreorder] int kmerScore; ^~~~~~~~~ /build/pizzly-0.37.3/common.h:17:7: warning: 'int ProgramOptions::insertSize' [-Wreorder] int insertSize; ^~~~~~~~~~ /build/pizzly-0.37.3/common.h:19:3: warning: when initialized here [-Wreorder] ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {} ^~~~~~~~~~~~~~ /build/pizzly-0.37.3/common.h:17:7: warning: 'ProgramOptions::insertSize' will be initialized after [-Wreorder] int insertSize; ^~~~~~~~~~ /build/pizzly-0.37.3/common.h:14:8: warning: 'bool ProgramOptions::ignoreProtein' [-Wreorder] bool ignoreProtein; ^~~~~~~~~~~~~ /build/pizzly-0.37.3/common.h:19:3: warning: when initialized here [-Wreorder] ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {} ^~~~~~~~~~~~~~ In file included from /build/pizzly-0.37.3/main.cpp:8: /build/pizzly-0.37.3/GeneModel.hpp: In member function 'bool Transcriptome::translateTrPosition(const string&, int, std::__cxx11::string&, int&, std::__cxx11::string&)': /build/pizzly-0.37.3/GeneModel.hpp:117:10: warning: unused variable 'fw' [-Wunused-variable] bool fw = (trxmodel.strand == Strandedness::FORWARD); ^~ /build/pizzly-0.37.3/GeneModel.hpp: In function 'void writeTranscriptome(Transcriptome&, std::ostream&)': /build/pizzly-0.37.3/GeneModel.hpp:146:17: warning: unused variable 'gene_id' [-Wunused-variable] const auto &gene_id = gene.first; ^~~~~~~ /build/pizzly-0.37.3/GeneModel.hpp:172:19: warning: unused variable 'tr_id' [-Wunused-variable] const auto &tr_id = trlist.first; ^~~~~ /build/pizzly-0.37.3/GeneModel.hpp: In function 'void parseGTF(Transcriptome&, const string&, const ProgramOptions&)': /build/pizzly-0.37.3/GeneModel.hpp:282:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(record.tagNames); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/GeneModel.hpp:329:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(record.tagNames); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/GeneModel.hpp:392:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(record.tagNames); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/pizzly-0.37.3/main.cpp:9: /build/pizzly-0.37.3/FilterFusions.hpp: At global scope: /build/pizzly-0.37.3/FilterFusions.hpp:116:2: warning: extra ';' [-Wpedantic] }; ^ In file included from /build/pizzly-0.37.3/main.cpp:9: /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:251:9: warning: unused variable 'matchlen' [-Wunused-variable] int matchlen = seqan::length(krseq); ^~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:311:19: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] if (tr_stop > seqan::length(trseq)) { ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:709:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ExonModel>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < trm.exons.size(); i++) { ~~^~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:738:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ExonModel>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < trm.exons.size(); i++) { ~~^~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:765:11: warning: unused variable 'gap' [-Wunused-variable] int gap = d2 - d1; ^~~ /build/pizzly-0.37.3/FilterFusions.hpp: In lambda function: /build/pizzly-0.37.3/FilterFusions.hpp:883:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < v.size(); i++) { ~~^~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:929:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < readsInTr.size(); i++) { ~~^~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:867:17: warning: unused variable 'split_reads' [-Wunused-variable] int split_reads = spp.second; ^~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:1091:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < readsInTr.size(); i++) { ~~^~~~~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:1115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < v.size(); i++) { ~~^~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:1112:18: warning: unused variable 'firstJsonRead' [-Wunused-variable] bool firstJsonRead = true; ^~~~~~~~~~~~~ /build/pizzly-0.37.3/main.cpp: In function 'int main(int, const char**)': /build/pizzly-0.37.3/main.cpp:126:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::unordered_map<std::__cxx11::basic_string<char>, seqan::String<char, seqan::Alloc<> > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] } else if (numTxpSeqFound != trx.seqs.size()) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/pizzly-0.37.3/main.cpp:8: /build/pizzly-0.37.3/GeneModel.hpp: In function 'Strandedness operator~(const Strandedness&)': /build/pizzly-0.37.3/GeneModel.hpp:18:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from /build/pizzly-0.37.3/main.cpp:9: /build/pizzly-0.37.3/FilterFusions.hpp: In function 'filterFusionRecord(const Transcriptome&, ProgramOptions&, const FusionRecord&, SplitRecord&)::<lambda(const string&, const std::vector<TranscriptPos>&, const std::vector<TranscriptPos>&, std::vector<std::pair<TranscriptPos, TranscriptPos> >&, int&)>': /build/pizzly-0.37.3/FilterFusions.hpp:389:22: warning: 'splitStrand' may be used uninitialized in this function [-Wmaybe-uninitialized] Strandedness splitStrand, safeStrand; ^~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp: In function 'bool filterFusionRecord(const Transcriptome&, ProgramOptions&, const FusionRecord&, SplitRecord&)': /build/pizzly-0.37.3/FilterFusions.hpp:603:25: warning: 'st2' may be used uninitialized in this function [-Wmaybe-uninitialized] splitrec.dir2 = st2 == Strandedness::FORWARD; // check read 2 ~~~~^~~~~~~~~~~~~~~ /build/pizzly-0.37.3/FilterFusions.hpp:602:25: warning: 'st1' may be used uninitialized in this function [-Wmaybe-uninitialized] splitrec.dir1 = st1 == Strandedness::FORWARD; // check read 1 ~~~~^~~~~~~~~~~~~~~ [100%] Linking CXX executable pizzly /usr/bin/cmake -E cmake_link_script CMakeFiles/pizzly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/pizzly-0.37.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -DSEQAN_HAS_ZLIB=1 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -rdynamic CMakeFiles/pizzly.dir/main.cpp.o -o pizzly -lpthread -lz make[3]: Leaving directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' [100%] Built target pizzly make[2]: Leaving directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/pizzly-0.37.3/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/pizzly-0.37.3/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/pizzly.substvars rm -fr -- debian/.debhelper/generated/pizzly/ debian/pizzly/ debian/tmp/ dh_auto_install install -d /build/pizzly-0.37.3/debian/pizzly debian/rules override_dh_install make[1]: Entering directory '/build/pizzly-0.37.3' help2man -N -n pizzly -s 1 obj-*/pizzly > debian/pizzly.1 dh_install install -d debian/pizzly/usr/bin cp --reflink=auto -a ./obj-x86_64-linux-gnu/pizzly debian/pizzly/usr/bin/ install -d debian/.debhelper/generated/pizzly make[1]: Leaving directory '/build/pizzly-0.37.3' dh_installdocs install -d debian/pizzly/usr/share/doc/pizzly cp --reflink=auto -a ./README.md debian/pizzly/usr/share/doc/pizzly cp --reflink=auto -a ./debian/README.source debian/pizzly/usr/share/doc/pizzly chown -R 0:0 debian/pizzly/usr/share/doc chmod -R u\+rw,go=rX debian/pizzly/usr/share/doc install -p -m0644 debian/copyright debian/pizzly/usr/share/doc/pizzly/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/pizzly/usr/share/doc/pizzly/changelog.Debian dh_installman install -d debian/pizzly/usr/share/man/man1/ install -p -m0644 ./debian/pizzly.1 debian/pizzly/usr/share/man/man1/pizzly.1 man -l --recode UTF-8 ./debian/pizzly/usr/share/man/man1/pizzly.1 > debian/pizzly/usr/share/man/man1/pizzly.1.dh-new mv debian/pizzly/usr/share/man/man1/pizzly.1.dh-new debian/pizzly/usr/share/man/man1/pizzly.1 chmod 0644 -- debian/pizzly/usr/share/man/man1/pizzly.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/pizzly chmod a-x usr/share/doc/pizzly/changelog.Debian usr/share/man/man1/pizzly.1 gzip -9nf usr/share/doc/pizzly/changelog.Debian usr/share/man/man1/pizzly.1 cd '/build/pizzly-0.37.3' dh_fixperms find debian/pizzly -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/pizzly ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/pizzly/usr/share/doc -type f -a -true -a ! -regex 'debian/pizzly/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pizzly/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/pizzly/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pizzly -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pizzly/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_strip install -d debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/pizzly/usr/bin/pizzly debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/e0/07af1a72a0a5e8fabbd532ad3c62f449415b58.debug chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/e0/07af1a72a0a5e8fabbd532ad3c62f449415b58.debug chown 0:0 -- debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/e0/07af1a72a0a5e8fabbd532ad3c62f449415b58.debug strip --remove-section=.comment --remove-section=.note debian/pizzly/usr/bin/pizzly objcopy --add-gnu-debuglink debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/e0/07af1a72a0a5e8fabbd532ad3c62f449415b58.debug debian/pizzly/usr/bin/pizzly install -d debian/.debhelper/pizzly/dbgsym-root/usr/share/doc ln -s pizzly debian/.debhelper/pizzly/dbgsym-root/usr/share/doc/pizzly-dbgsym dh_makeshlibs rm -f debian/pizzly/DEBIAN/shlibs dh_shlibdeps install -d debian/pizzly/DEBIAN dpkg-shlibdeps -Tdebian/pizzly.substvars debian/pizzly/usr/bin/pizzly dh_installdeb dh_gencontrol echo misc:Depends= >> debian/pizzly.substvars echo misc:Pre-Depends= >> debian/pizzly.substvars install -d debian/.debhelper/pizzly/dbgsym-root/DEBIAN dpkg-gencontrol -ppizzly -ldebian/changelog -Tdebian/pizzly.substvars -Pdebian/.debhelper/pizzly/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=pizzly-dbgsym "-DDepends=pizzly (= \${binary:Version})" "-DDescription=debug symbols for pizzly" -DBuild-Ids=e007af1a72a0a5e8fabbd532ad3c62f449415b58 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppizzly -ldebian/changelog -Tdebian/pizzly.substvars -Pdebian/pizzly -UMulti-Arch chmod 0644 -- debian/pizzly/DEBIAN/control chown 0:0 -- debian/pizzly/DEBIAN/control dh_md5sums cd debian/pizzly >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/pizzly/DEBIAN/md5sums chown 0:0 -- debian/pizzly/DEBIAN/md5sums cd debian/.debhelper/pizzly/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/pizzly .. dpkg-deb --build debian/.debhelper/pizzly/dbgsym-root .. dpkg-deb: building package 'pizzly-dbgsym' in '../pizzly-dbgsym_0.37.3-1_amd64.deb'. dpkg-deb: building package 'pizzly' in '../pizzly_0.37.3-1_amd64.deb'. dpkg-genbuildinfo dpkg-genchanges >../pizzly_0.37.3-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source --after-build . dpkg-buildpackage: info: full upload (original source is included) [0mI: Copying back the cached apt archive contents[0m [0mI: unmounting /var/cache/pbuilder/ccache filesystem[0m [0mI: unmounting /home/satta/_pbuilder_local_deps filesystem[0m [0mI: unmounting /dev/shm filesystem[0m [0mI: unmounting dev/ptmx filesystem[0m [0mI: unmounting dev/pts filesystem[0m [0mI: unmounting dev/shm filesystem[0m [0mI: unmounting proc filesystem[0m [0mI: unmounting sys filesystem[0m [0mI: Current time: Tue Jun 4 12:27:10 CEST 2019[0m [0mI: pbuilder-time-stamp: 1559644030[0m [0mI: Cleaning COW directory[0m [0mI: forking: rm -rf /var/cache/pbuilder/build/cow.22563[0m
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