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 <[email protected]>
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 <[email protected]>
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
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[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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