[Debian-med-packaging] Bug#1075617: velvet: ftbfs with GCC-14

Matthias Klose doko at debian.org
Wed Jul 3 13:47:22 BST 2024


Package: src:velvet
Version: 1.2.10+dfsg1-8
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie 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-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/velvet_1.2.10+dfsg1-8_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html

[...]
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o 
In file included from src/passageMarker.c:29:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o 
In file included from src/graphStats.c:28:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o 
In file included from src/correctedGraph.c:26:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
  178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
  177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
  174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
  173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o 
src/readSet.c: In function ‘readFastXFile’:
src/readSet.c:641:21: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
  641 |         file.gzFile = file.autoFile = NULL;
      |                     ^
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
  680 |         file1.gzFile = file1.autoFile = NULL;
      |                      ^
src/readSet.c:681:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
  681 |         file2.gzFile = file2.autoFile = NULL;
      |                      ^
make[2]: *** [Makefile:109: obj/readSet.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS=-Wl,-z,relro returned exit code 2
make[1]: *** [debian/rules:25: build_long_versions] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2



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