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 '/<<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.
