[Debian-med-packaging] Bug#957846: subread: ftbfs with GCC-10

Fri Apr 17 12:11:38 BST 2020

Package: src:subread
Version: 2.0.0+dfsg-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/subread_2.0.0+dfsg-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
   dh_autoreconf
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o core.o core.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o core-junction.o core-junction.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o core-indel.o core-indel.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o sambam-file.o sambam-file.c
In file included from /usr/include/string.h:495,
                 from sambam-file.c:30:
In function ‘strncpy’,
    inlined from ‘PBam_chunk_headers’ at sambam-file.c:560:6:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 100 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o sublog.o sublog.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gene-algorithms.o gene-algorithms.c
In file included from /usr/include/string.h:495,
                 from gene-algorithms.c:26:
In function ‘strncpy’,
    inlined from ‘bad_reverse_cigar’ at gene-algorithms.c:2583:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncat’,
    inlined from ‘bad_reverse_cigar’ at gene-algorithms.c:2575:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
  136 |   return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘bad_reverse_cigar’ at gene-algorithms.c:2576:4:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o hashtable.o hashtable.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o input-files.o input-files.c
input-files.c: In function ‘is_SAM_unsorted’:
input-files.c:6213:33: warning: ‘read_name[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 6213 |  for(field_cursor = 0; read_name[field_cursor] ; field_cursor++)
      |                        ~~~~~~~~~^~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o sorted-hashtable.o sorted-hashtable.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gene-value-index.o gene-value-index.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o exon-algorithms.o exon-algorithms.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o HelperFunctions.o HelperFunctions.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o interval_merge.o interval_merge.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o long-hashtable.o long-hashtable.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o core-bigtable.o core-bigtable.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o seek-zlib.o seek-zlib.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o input-blc.o input-blc.c
gcc -O3 -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\"  -D_FILE_OFFSET_BITS=64  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -mtune=generic -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now  -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
/usr/bin/ld: core.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: core-junction.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: core-indel.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: sambam-file.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: gene-algorithms.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: input-files.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: sorted-hashtable.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: gene-value-index.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: HelperFunctions.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: core-bigtable.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: seek-zlib.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
/usr/bin/ld: input-blc.o:./src/gene-algorithms.h:63: multiple definition of `replica_index'; /tmp/ccl3sl9d.o:./src/gene-algorithms.h:63: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile.Linux:41: genRandomReads] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [debian/rules:32: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:25: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2