Your message dated Thu, 19 Dec 2024 14:47:08 +0100
with message-id <z2qj3eix0riem...@an3as.eu>
and subject line Forgot to add "Closes: #1089249" in changelog of allelecount
4.3.0-3
has caused the Debian Bug report #1089249,
regarding allelecount: FTBFS with make 4.4.1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1089249: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1089249
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:allelecount
Version: 4.3.0-2
User: debian...@lists.debian.org
Usertags: make-4.4
Severity: important
Tags: ftbfs
Dear Maintainer,
This package fails to build from source with Make 4.4.1, most likely because of
changes in $(shell) environment handling: environment variables exported from
Makefiles are now made available to commands invoked using $(shell), which
can cause issues with recursive definitions in particular. See
https://salsa.debian.org/debian/make/-/blob/master/debian/NEWS for a complete
list of backward-incompatible changes since Make 4.3.
Below you will find how the builds end, hopefully the most relevant
part from the build log. A full build log is available here:
https://people.debian.org/~sanvila/make-4.4/build-logs/
Make 4.4.1 is currently available in experimental and will hopefully
soon be uploaded to unstable, at which time this bug will become
release-critical.
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Please reach out to the Make maintainer, Stephen Kitt <sk...@debian.org> if
you need help fixing this.
--------------------------------------------------------------------------------
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure --sourcedirectory=c
dh_auto_configure --sourcedirectory=perl
cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wl,-z,relro -Wl,-z,now"
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for alleleCount
Writing MYMETA.yml and MYMETA.json
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=c
cd c && make -j2 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/c'
rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log
./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov
*.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
mkdir -p ./bin
mkdir -p ./htslib_tmp
#Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather
than libhts.so
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection
-Wformat -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic
-c src/bam_access.c -o src/bam_access.o
ln -fs /libhts.a ./htslib_tmp/libhts.a
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection
-Wformat -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic
./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib
-Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now tests/bam_access_tests.c -o
tests/bam_access_tests
tests/bam_access_tests.c: In function
‘test_bam_access_get_position_base_counts’:
tests/bam_access_tests.c:45:13: warning: variable ‘res’ set but not used
[-Wunused-but-set-variable]
45 | int res =
bam_access_get_position_base_counts(chr,pos,stats,0,NULL);
| ^~~
/usr/bin/ld: cannot find ./src/bam_access.o: No such file or directory
collect2: error: ld returned 1 exit status
make[2]: *** [<builtin>: tests/bam_access_tests] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/c'
dh_auto_build: error: cd c && make -j2 "INSTALL=install --strip-program=true"
returned exit code 2
make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Hi
unfortunatel I forgot to add "Closes: #1089249" in changelog of allelecount
4.3.0-3.
Closing this bug manually
Andreas.
--
https://fam-tille.de
--- End Message ---
