Your message dated Fri, 09 Oct 2020 13:34:07 +0000 with message-id <[email protected]> and subject line Bug#966876: fixed in trinityrnaseq 2.11.0+dfsg-1 has caused the Debian Bug report #966876, regarding trinityrnaseq: FTBFS: sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of ‘std’ to be marked as done.
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--- Begin Message ---Source: trinityrnaseq Version: 2.10.0+dfsg-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200802 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro > -Wl,-z,now sift_bam_max_cov.cpp -Wall -lhts -O2 -o bamsifter > sift_bam_max_cov.cpp: In function ‘int main(int, char**)’: > sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of ‘std’ > 99 | std::string tmp_text(input_header->text, input_header->l_text); > | ^~~~~~ > sift_bam_max_cov.cpp:16:1: note: ‘std::string’ is defined in header > ‘<string>’; did you forget to ‘#include <string>’? > 15 | #include "htslib/bgzf.h" > +++ |+#include <string> > 16 | > sift_bam_max_cov.cpp:100:24: error: ‘tmp_text’ was not declared in this scope > 100 | size_t start_pos = tmp_text.find("@HD"); > | ^~~~~~~~ > sift_bam_max_cov.cpp:101:27: error: ‘std::string’ has not been declared > 101 | if (start_pos == std::string::npos) { > | ^~~~~~ > sift_bam_max_cov.cpp:106:25: error: ‘std::string’ has not been declared > 106 | if (end_pos == std::string::npos) { > | ^~~~~~ > sift_bam_max_cov.cpp:111:27: error: ‘std::string’ has not been declared > 111 | if (start_pos == std::string::npos) { > | ^~~~~~ > sift_bam_max_cov.cpp:116:27: error: ‘std::string’ has not been declared > 116 | if (start_pos == std::string::npos) { > | ^~~~~~ > sift_bam_max_cov.cpp:144:19: error: ‘string’ is not a member of ‘std’ > 144 | std::set<std::string> mates_to_keep[input_header->n_targets]; > | ^~~~~~ > sift_bam_max_cov.cpp:144:19: note: ‘std::string’ is defined in header > ‘<string>’; did you forget to ‘#include <string>’? > sift_bam_max_cov.cpp:144:19: error: ‘string’ is not a member of ‘std’ > sift_bam_max_cov.cpp:144:19: note: ‘std::string’ is defined in header > ‘<string>’; did you forget to ‘#include <string>’? > sift_bam_max_cov.cpp:144:25: error: template argument 1 is invalid > 144 | std::set<std::string> mates_to_keep[input_header->n_targets]; > | ^ > sift_bam_max_cov.cpp:144:25: error: template argument 2 is invalid > sift_bam_max_cov.cpp:144:25: error: template argument 3 is invalid > sift_bam_max_cov.cpp:160:48: error: request for member ‘clear’ in > ‘mates_to_keep[current_rname_index]’, which is of non-class type ‘int’ > 160 | mates_to_keep[current_rname_index].clear(); > | ^~~~~ > sift_bam_max_cov.cpp:205:43: error: request for member ‘find’ in > ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::tid]’, which is of non-class > type ‘int’ > 205 | (mates_to_keep[aln->core.tid].find(bam_get_qname(aln)) != > mates_to_keep[aln->core.tid].end())) { > | ^~~~ > sift_bam_max_cov.cpp:205:100: error: request for member ‘end’ in > ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::tid]’, which is of non-class > type ‘int’ > 205 | (mates_to_keep[aln->core.tid].find(bam_get_qname(aln)) != > mates_to_keep[aln->core.tid].end())) { > | > ^~~ > sift_bam_max_cov.cpp:249:47: error: request for member ‘insert’ in > ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::mtid]’, which is of non-class > type ‘int’ > 249 | > mates_to_keep[aln->core.mtid].insert(bam_get_qname(aln)); > | ^~~~~~ > make[2]: *** [Makefile:3: sift_bam_max_cov] Error 1 The full build log is available from: http://qa-logs.debian.net/2020/08/02/trinityrnaseq_2.10.0+dfsg-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: trinityrnaseq Source-Version: 2.11.0+dfsg-1 Done: [email protected] (Michael R. Crusoe) We believe that the bug you reported is fixed in the latest version of trinityrnaseq, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <[email protected]> (supplier of updated trinityrnaseq 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 09 Oct 2020 15:13:36 +0200 Source: trinityrnaseq Architecture: source Version: 2.11.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Michael R. Crusoe <[email protected]> Closes: 966876 Changes: trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Fix gcc-10 build issue Closes: #966876 * debhelper-compat 13 (routine-update) * Review Files-Excluded for moved and removed files as well as new binary *.jars * Remove redundant debian/gbp.conf * Remove __pycache__ from installed package . [ Michael R. Crusoe ] * Correct location of bamsifter installation * debian/patches/fix_system_paths: fix expected path for ParaFly * debian/patches/update-paths: fix paths to Butterfly.jar * Enable more features and tests with r-cran-{argparse,dexseq} & tabix Checksums-Sha1: 94a7a42720b572bf821ec2dba0f0b80a0482cd1d 2650 trinityrnaseq_2.11.0+dfsg-1.dsc 833cd913ce9c7f864a6fa240268225cd1d6bd04e 258759712 trinityrnaseq_2.11.0+dfsg.orig.tar.xz e54e4b941f72fab55ee207e097928c350a3ede05 151332 trinityrnaseq_2.11.0+dfsg-1.debian.tar.xz 5a87cd88aedb13bd5d1e37e5311e5e50e82e67f8 17267 trinityrnaseq_2.11.0+dfsg-1_source.buildinfo Checksums-Sha256: 9039fe7880f3d87f752688147bcad7481c213f23f974317911d64f91c349381e 2650 trinityrnaseq_2.11.0+dfsg-1.dsc 78a9de6063044c5880196d706ad23e8db437795df26eb0b521e386a4146356d0 258759712 trinityrnaseq_2.11.0+dfsg.orig.tar.xz b38df405b6d0e1a99011a2f77bb90d58091b82b79ea80b50e1f0fdd9bfddc4c8 151332 trinityrnaseq_2.11.0+dfsg-1.debian.tar.xz a47a54c21395d60dbee1a9b30463681d980f43c692d37066c5ef03d03a55799a 17267 trinityrnaseq_2.11.0+dfsg-1_source.buildinfo Files: d08d6f1a254462e85d61993c8a75deb3 2650 science optional trinityrnaseq_2.11.0+dfsg-1.dsc a877bd080145ccb922f3906dcd5e9efc 258759712 science optional trinityrnaseq_2.11.0+dfsg.orig.tar.xz 5d7754b3f09a7b0a3e5904ea41aeb80f 151332 science optional trinityrnaseq_2.11.0+dfsg-1.debian.tar.xz 0f97057a7361c71af17b3befa16d8a01 17267 science optional trinityrnaseq_2.11.0+dfsg-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl+AYwwACgkQPCZ2P2xn 5uIBxQ//cRfB8BBpD6XvwWIqYu0YmciKP8F+DFlWJF8F88MaJDvoEKzudb1GVIiQ rUX4wInuqSWd/6oZEhDqPnEKhdjYFeLnUHA3ku4GXXJZPhAYBwxqmISJ3S7uM+VL jrDCvDvaBhZco+9klRVT/fMj2tuCahb4cQep5qwvIVqD0Dz8MNW9HADO0Jpl2LOU yXz62on0RheRe1MDIhMFnIFHJGiYKPpZbEljDa//gX3e8xuiW5ognWdvG7Arp4nc SunUNDW65T+3mU2tvc+8xi7U/w5frVDoCvzfS4RT4F7CN0JQ+2RO+t7c1wWnj6Aj HZWVqxUerIX6Ae874IZfRxSStQxT8pW/cdSm5JXcVD5Q90gqoyYF1DuFLHNXiBdG PjYejp7u/+QeEBCMBCBonHi+qyJDPFfVmI8Ma/uPR1+G48tv9nZzV3Eon2z+C/M9 a2rbXTR4os4lVUrcrHJbNEeveUM389tMH2N0qh+5jzD9wNKPiqnk515uWSjRvUmq mZZptILDut/IA79ejRi3jBvE5cx8YWT9KlROMwP8sbDsQOgbMYfewFFAneWcwK5U LRZBBzJBRzCpqovqUluGcCno6vig/z2PEzl8lq66z/FGkSBWivsmq42mwGbBH9xQ b63Eeg2WDJS4jeKzibuCD5y6yBvDyDBiGV0bKYUhbNJ6t0zrOhk= =F2Sa -----END PGP SIGNATURE-----
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