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

[Andreas Tille]

Hi Lucas,

thanks for your QA effort.

On Wed, May 02, 2018 at 10:53:42PM +0200, Lucas Nussbaum wrote:
> > 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

while this issue seems totally unrelated to the new upstream version of
BioConductor packages I will upload all preconditions for the new
version first and check the issue in the new version.

Kind regards

       Andreas.

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