Package: src:snippy Version: 4.6.0+dfsg-4 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_test make[1]: Entering directory '/<<PKGBUILDDIR>>' cd test && /usr/bin/make make[2]: Entering directory '/<<PKGBUILDDIR>>/test' mkdir -p S1 wgsim -S 1 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ example.fna S1/R1.fq S1/R1.fq > S1/dwgsim.tab [wgsim] seed = 1 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 Makefile:35: warning: pattern recipe did not update peer target 'S1/R2.fq'. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq [21:16:23] This is snippy 4.6.0 [21:16:23] Written by Torsten Seemann [21:16:23] Obtained from https://github.com/tseemann/snippy [21:16:23] Detected operating system: linux [21:16:23] Enabling bundled linux tools. [21:16:23] Found bwa - /usr/bin/bwa [21:16:23] Found bcftools - /usr/bin/bcftools [21:16:23] Found samtools - /usr/bin/samtools [21:16:23] Found java - /usr/bin/java [21:16:23] Found snpEff - /usr/bin/snpEff [21:16:23] Found samclip - /usr/bin/samclip [21:16:23] Found seqtk - /usr/bin/seqtk [21:16:23] Found parallel - /usr/bin/parallel [21:16:23] Found freebayes - /usr/bin/freebayes [21:16:23] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel [21:16:23] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py [21:16:23] Found vcfstreamsort - /usr/bin/vcfstreamsort [21:16:23] Found vcfuniq - /usr/bin/vcfuniq [21:16:23] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader [21:16:23] Found gzip - /usr/bin/gzip [21:16:23] Found vt - /usr/bin/vt [21:16:23] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab [21:16:23] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report [21:16:23] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [21:16:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 [21:16:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 [21:16:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 [21:16:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [21:16:23] Using reference: /<<PKGBUILDDIR>>/test/example.fna [21:16:23] Treating reference as 'fasta' format. [21:16:23] Will use 2 CPU cores. [21:16:23] Can not read sequence file: S1/R2.fq make[2]: *** [Makefile:32: S1/snps.tab] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/test' make[1]: *** [debian/rules:10: override_dh_auto_test] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:6: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
