[Debian-med-packaging] Bug#984106: libgenome: ftbfs with GCC-11

Wed Mar 3 16:14:22 GMT 2021

Package: src:libgenome
Version: 1.3.11+svn20110227.4616-3
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libgenome_1.3.11+svn20110227.4616-3_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
 /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
 /usr/bin/install -c -m 644 libGenome.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
# Call d-shlibmove to comply with library packaging guide
# mv debian/tmp/usr/include/*/* debian/tmp/usr/include/
d-shlibmove --commit \
            --multiarch \
	    --devunversioned \
	    --exclude-la \
	    --movedev debian/tmp/usr/include/* usr/include \
	    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/x86_64-linux-gnu/pkgconfig \
	    debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libgenome-dev/usr/lib/x86_64-linux-gnu
install -d -m 755 debian/libgenome0/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libGenome.a debian/libgenome-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libGenome.so debian/libgenome-dev/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libGenome.so.0 debian/libgenome0/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libGenome.so.0.1.3 debian/libgenome0/usr/lib/x86_64-linux-gnu
PKGDEV=libgenome-dev
PKGSHL=libgenome0
install -d -m 755 debian/libgenome-dev/usr/include
mv debian/tmp/usr/include/libGenome debian/libgenome-dev/usr/include
install -d -m 755 debian/libgenome-dev/usr/lib/x86_64-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libgenome-dev/usr/lib/x86_64-linux-gnu/pkgconfig
find debian -name libGenome.la -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs
   dh_installchangelogs
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libgenome0/DEBIAN/symbols doesn't match completely debian/libgenome0.symbols.amd64

--- debian/libgenome0.symbols.amd64 (libgenome0_1.3.11+svn20110227.4616-3_amd64)
+++ dpkg-gensymbolstp7952	2021-03-01 21:07:22.362888236 +0000
@@ -630,7 +630,7 @@
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-3# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS5_S7_EERSA_ at Base 1.3.11+svn20110227.4616
@@ -660,6 +660,8 @@
  _ZNSt7__cxx1110_List_baseINS_12basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
  _ZNSt7__cxx1110_List_baseIPKN6genome12gnBaseFilterESaIS4_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
  (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 1.3.11+svn20110227.4616-3
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 1.3.11+svn20110227.4616-3
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE16_M_insert_uniqueISB_EES6_ISt17_Rb_tree_iteratorISB_EbEOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE20_Reuse_or_alloc_nodeclIRKS8_EEPSt13_Rb_tree_nodeIS8_EOT_ at Base 1.3.11+svn20110227.4616
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

