Package: src:allelecount Version: 4.3.0-2 User: [email protected] 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 <[email protected]> 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 --------------------------------------------------------------------------------
