Bug#897540: r-bioc-variantannotation: FTBFS: g++: error: /libtabix.a: No such file or directory
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. -- http://fam-tille.de
Bug#897540: r-bioc-variantannotation: FTBFS: g++: error: /libtabix.a: No such file or directory
Source: r-bioc-variantannotation Version: 1.24.5-1 Severity: serious Tags: buster sid User: debian...@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 '/<>/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 >