Your message dated Thu, 03 May 2018 18:52:02 +0000 with message-id <e1fejkk-000fd6...@fasolo.debian.org> and subject line Bug#897540: fixed in r-bioc-variantannotation 1.26.0-1 has caused the Debian Bug report #897540, regarding r-bioc-variantannotation: FTBFS: g++: error: /libtabix.a: No such file or directory to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 897540: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897540 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
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--- Begin Message ---Source: r-bioc-variantannotation Source-Version: 1.26.0-1 We believe that the bug you reported is fixed in the latest version of r-bioc-variantannotation, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 897...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated r-bioc-variantannotation package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 03 May 2018 20:16:50 +0200 Source: r-bioc-variantannotation Binary: r-bioc-variantannotation Architecture: source Version: 1.26.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: r-bioc-variantannotation - BioConductor annotation of genetic variants Closes: 897540 Changes: r-bioc-variantannotation (1.26.0-1) unstable; urgency=medium . * New upstream version Closes: #897540 * dh-update-R to update Build-Depends * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 Checksums-Sha1: 7be086a18c2690e2227c079d6ae892f26078f5cb 2672 r-bioc-variantannotation_1.26.0-1.dsc e10a0745e6191b52ce9aeef9bbf8a7bccbbf674c 1719754 r-bioc-variantannotation_1.26.0.orig.tar.gz f493d1f90983bd21e00049a4a7ba90d1b62c4197 7560 r-bioc-variantannotation_1.26.0-1.debian.tar.xz 07f17c2941bb025a9b63643f9b4fcb7f59bb8e9f 10487 r-bioc-variantannotation_1.26.0-1_amd64.buildinfo Checksums-Sha256: daa214cf8386361f6a4e6bfac892afcb1dff0d41dafd2afccdbda657f15a5dc7 2672 r-bioc-variantannotation_1.26.0-1.dsc c7b26a281105495790b0fda335f07896d3340a61af42364c3d4aee535c636c19 1719754 r-bioc-variantannotation_1.26.0.orig.tar.gz 7648c84efad21d3e520b6ed30abcd4a5b914324e4b25cdfd9780a678d61477e7 7560 r-bioc-variantannotation_1.26.0-1.debian.tar.xz 4abd21277fe1de08fd738b3597d5c01a5c3fceb870143534ff8c0a73e9d235b8 10487 r-bioc-variantannotation_1.26.0-1_amd64.buildinfo Files: 06981dcff3c97d71e0705fa254047975 2672 gnu-r optional r-bioc-variantannotation_1.26.0-1.dsc 0ac5c3fb619e6203e54388cc4a71a8c7 1719754 gnu-r optional r-bioc-variantannotation_1.26.0.orig.tar.gz c0fbc80327b1ea62c5a16b899916cbfe 7560 gnu-r optional r-bioc-variantannotation_1.26.0-1.debian.tar.xz b5dc31ed0d85b8fcdba4054deea101ee 10487 gnu-r optional r-bioc-variantannotation_1.26.0-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlrrVRcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGVzw//YjzuvfqJnDDP/OtrwaZzCGTzoInyTXGh vEXC+JO5IgJ5m+VHJeRa4NCJ+NebSx930BkHBQ5LFpczNaQYOCY7L1IIUYUTrYYQ 2kL8e80i5grBMA56vukqs9mntJeDFG9fZqMV8eWZoR54uJv9lg32QAWaDd/rZAuo eUeYxVb1qRIO5Bn2JlRZCrMjKy0QJSyu8mz0AWZmeFeV1kuLboEUkvd+xjMhBI+d atXSjkydSf3j9AnGJnGUQmHecp/1QPZDg1yA4o2u1hHdEX7TvyorCISIX8k/dXG3 8l5rGY1bpR1EwxmWkP3+aObwr1U2bf0qErTLqlu+di75lGXHeJDvrYf8dcDzYzM8 Y8Gl9b1DhL65kxB5F0CVZrqN4F8l7e40/QDWJPWE1iC1jQXL/1/NrMDGRZkpYA0a uBDmwSYLiN8FjVE2+ml3at8wSWE+gX1rr8GGF8mww9NTJ/zixogTA48UvBaGUP75 XTb0alE4eqqFWAZq7uds3QVR2RBfze5fGHaoLwurHs9WGpaUKwWke2GJhAtqFwbi FR0+UoWWHlTHZr3PiY6y14oKjWOPgQcFPEHgKfSYKaDYg5HNW9791FSR/t6Z/rYR otJZrvNVRNm9pShM+/roos1d8uD5YfEAMYYN3fbM5QHx/298bT8dGP77yQonP1Kn hIYYAffZWuA= =2gr9 -----END PGP SIGNATURE-----
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