[Debian-med-packaging] Bug#910324: freebayes parallel FTBFS

[Helmut Grohne]

Source: freebayes
Version: 1.2.0-1
Severity: serious
Tags: ftbfs

freebayes fails to build from source in sbuild on unstable/amd64 when
performing a parallel build. The linker invocation is run before all
relevant objects are compiled. A build log ends with:

| g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../ttmath  -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` bamleftalign.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/bamleftalign -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
| g++: error: AlleleParser.o: No such file or directory
| g++: error: Genotype.o: No such file or directory
| g++: error: ResultData.o: No such file or directory
| make[2]: *** [Makefile:81: ../bin/bamleftalign] Error 1
| make[2]: *** Waiting for unfinished jobs....
| make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
| make[1]: *** [Makefile:2: all] Error 2
| make[1]: Leaving directory '/<<PKGBUILDDIR>>'
| dh_auto_build: make -j12 "INSTALL=install --strip-program=true" returned exit code 2
| make: *** [debian/rules:6: build] Error 2
| dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2

The issue is also seen during reproducible builds:

https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/freebayes_1.2.0-1.rbuild.log.gz

Helmut