[Debian-med-packaging] Bug#897540: r-bioc-variantannotation: FTBFS: g++: error: /libtabix.a: No such file or directory

[Lucas Nussbaum]

Source: r-bioc-variantannotation
Version: 1.24.5-1
Severity: serious
Tags: buster sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20180502 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dna_hash.c -o dna_hash.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rle.c -o rle.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strhash.c -o strhash.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vcffile.c -o vcffile.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vcftype.c -o vcftype.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c writevcf.c -o writevcf.o
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /libbam.a /libbcf.a /libtabix.a -lz -pthread -L/usr/lib/R/lib -lR
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> Error: Functions found when exporting methods from the namespace 'IRanges' which are not S4 generic: 'endoapply', 'mendoapply'
> Execution halted
> g++: error: /libbam.a: No such file or directory
> g++: error: /libbcf.a: No such file or directory
> g++: error: /libtabix.a: No such file or directory
> make[1]: *** [/usr/share/R/share/make/shlib.mk:6: VariantAnnotation.so] Error 1

The full build log is available from:
   http://aws-logs.debian.net/2018/05/02/r-bioc-variantannotation_1.24.5-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.