Your message dated Fri, 17 Jun 2016 13:49:16 +0000 with message-id <e1bdu96-0005tc...@franck.debian.org> and subject line Bug#826304: fixed in gmap 2016-06-09-1 has caused the Debian Bug report #826304, regarding gmap: FTBFS in sid: 3 test fail 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.) -- 826304: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=826304 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: gmap Version: 2016-05-25-1 Severity: serious Justification: fails to build from source Hi, gmap FTBFS in sid with testsuite failures: dh_auto_test -O--parallel make -j16 check VERBOSE=1 make[1]: Entering directory '/build/gmap-2016-05-25' Making check in src make[2]: Entering directory '/build/gmap-2016-05-25/src' make[2]: Leaving directory '/build/gmap-2016-05-25/src' Making check in util make[2]: Entering directory '/build/gmap-2016-05-25/util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/gmap-2016-05-25/util' Making check in tests make[2]: Entering directory '/build/gmap-2016-05-25/tests' make check-TESTS make[3]: Entering directory '/build/gmap-2016-05-25/tests' make[4]: Entering directory '/build/gmap-2016-05-25/tests' FAIL: iit.test FAIL: coords1.test FAIL: setup1.test PASS: align.test =========================================== gmap 2016-05-25: tests/test-suite.log =========================================== # TOTAL: 4 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 3 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: coords1 ============= Cannot write to file coords.chr17test at /build/gmap-2016-05-25/util/fa_coords line 118. Opening file /build/gmap-2016-05-25/tests/ss.chr17test Processed short contigs (<1000000 nt): .diff: coords.chr17test: No such file or directory FAIL coords1.test (exit status: 2) FAIL: setup1 ============ Sorting chromosomes in chrom order. To turn off or sort other ways, use the -s flag. Could not create ./chr17test.sources at /build/gmap-2016-05-25/util/gmap_build line 155. diff: ./chr17test/chr17test.genomecomp: No such file or directory Difference found between chr17test.genomecomp and setup.genomecomp.ok FAIL setup1.test (exit status: 1) FAIL: iit ========= mkdir: cannot create directory 'testSubDir': File exists Finished reading FASTA file -- total entries: 3 Maximum coordinate: 40000 Total label length: 3 + 3 separators Total annotation length: 80 + 3 separators Saw 0 distinct divisions/chromosomes Saw 3 distinct tags/types No divs/chromosomes provided, so storing as IIT version 1 Error: can't open file iittest.iit ./iit.test: line 12: iit_get.out: No such file or directory diff: iit_get.out: No such file or directory ./iit.test: line 15: iit_dump.out: No such file or directory diff: iit_dump.out: No such file or directory FAIL iit.test (exit status: 2) ============================================================================ Testsuite summary for gmap 2016-05-25 ============================================================================ # TOTAL: 4 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 3 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log Please report to Thomas Wu <t...@gene.com> ============================================================================ Makefile:575: recipe for target 'test-suite.log' failed make[4]: *** [test-suite.log] Error 1 make[4]: Leaving directory '/build/gmap-2016-05-25/tests' Makefile:681: recipe for target 'check-TESTS' failed make[3]: *** [check-TESTS] Error 2 make[3]: Leaving directory '/build/gmap-2016-05-25/tests' Makefile:747: recipe for target 'check-am' failed make[2]: *** [check-am] Error 2 make[2]: Leaving directory '/build/gmap-2016-05-25/tests' Makefile:430: recipe for target 'check-recursive' failed make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory '/build/gmap-2016-05-25' dh_auto_test: make -j16 check VERBOSE=1 returned exit code 2 debian/rules:19: recipe for target 'build' failed make: *** [build] Error 2 Andreas
gmap_2016-05-25-1.log.gz
Description: application/gzip
--- End Message ---
--- Begin Message ---Source: gmap Source-Version: 2016-06-09-1 We believe that the bug you reported is fixed in the latest version of gmap, 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 826...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alexandre Mestiashvili <a...@biotec.tu-dresden.de> (supplier of updated gmap 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: SHA256 Format: 1.8 Date: Wed, 08 Jun 2016 16:36:13 +0200 Source: gmap Binary: gmap Architecture: source amd64 Version: 2016-06-09-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Alexandre Mestiashvili <a...@biotec.tu-dresden.de> Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Closes: 826304 Changes: gmap (2016-06-09-1) unstable; urgency=medium . * Add links to binaries for specific CPU instruction sets (ssse4.1 and nosimd) * Override lintian warnings for missing man pages * Imported Upstream version 2016-06-03 2016-06-09 * Don't run dh_auto_test in parallel, Closes: #826304 Checksums-Sha1: 0f2b6fb35cb3e5049f3631a0ecb2bc8a826ff71a 2065 gmap_2016-06-09-1.dsc 1e8bd2faf9e2cd02acb5d5aa1a5589f33acc65eb 2936520 gmap_2016-06-09.orig.tar.xz 636da6eab6cc26872de8f889ec6f88c6cdbe935c 7160 gmap_2016-06-09-1.debian.tar.xz a4112009a285e09d5f3b5ece0e8018ca4b964877 14083154 gmap-dbgsym_2016-06-09-1_amd64.deb f3baf3a63dcde3fcff402fa475f312cf7fe437a7 18937908 gmap_2016-06-09-1_amd64.deb Checksums-Sha256: 4d2c1699e08c6f0de0e1a044bbb1e7e99e0295100c7adf0e982ea14dc4b63b79 2065 gmap_2016-06-09-1.dsc e0ff28cd4736e47a3fd0cd0790376af3abfd1f537596deb9ca31f38669b22fce 2936520 gmap_2016-06-09.orig.tar.xz 31b540b381e8704324515126052a38beeffe51381275a445a2328df3e6197b6d 7160 gmap_2016-06-09-1.debian.tar.xz 6b57e8332b3e2ecb6f083933cff8fc9e40d3e02fa68333f86cf9fc446b565e60 14083154 gmap-dbgsym_2016-06-09-1_amd64.deb b78358a2ff931daea4a7b6bc1ddb9a9335195445819d60304c09eced8b90ca47 18937908 gmap_2016-06-09-1_amd64.deb Files: 9fd67b254bef8a722d27f623191c627f 2065 non-free/science optional gmap_2016-06-09-1.dsc 4beb231c94dc636198fc286358a47fc1 2936520 non-free/science optional gmap_2016-06-09.orig.tar.xz 276ecb71c8504cfc8363a0b8d705eed7 7160 non-free/science optional gmap_2016-06-09-1.debian.tar.xz 32c867cdde5194b76b3434e9a3f7646e 14083154 non-free/debug extra gmap-dbgsym_2016-06-09-1_amd64.deb 6884a20abd65f42714a1db1e3982d6d6 18937908 non-free/science optional gmap_2016-06-09-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXY/YVAAoJEBz3khEbUiiwU60P/1i23+3SpTeOKS+td32hYDRs QpOQgYaP/lLd3s/W+eVGpv+/W162QNiiO2qoVLaXNwH6Pbz3oYmyyGVF/lP+G9gj lRJsAZpfhrYQumqg9A8W5cvtDU9op94ZGRUDQ1jK18C69kwtSjw5RT/hUN8v563M Xm7cQMd62KbYENWSFEfExHLFM25h/uB5gntDMI1a7Cb9d3nkDQ3QTy/aL9io4P5D XUosk5r1S4/fw8Pu60CZsZxYkgkn163KUCf6hFyzJozw0L1pO2WrCp2j/NQTsHUM c4k+MCujQPg39wMl8demmBbQuR4XBxS6tqYXw6a4GaRGWm07kybc1aKwOWNsdnIF HrJC9e1fMyet7W/SsOxl+YfsXyQx/PjDuQyHdInX7E0G6Mvpqos9NHUz2bW49ZiP fXW/TlCpPuWRSwZjLMZ9A64D9/A8zBWEYuzzpX3C6YAXaedbxFhS0sHLw8VWVhJH puV2maVqvFReWaxUXO8Mcyc8B0Zw2L4MCMzHu/+9DZkK8QKuGGcWv84sXytZpXJZ ws5m8NB1DUZee36aowHYsaGrOJKGZJdzeQBwgWMXkri0MgpZD6CPK/JBJ61DaN8s OwRNQnaC2/ORVIHx2JJN0/J32q+TQ4sZjFF8ji/zDWF6qkgw6QjOAqbyXsmjvcWJ ZjRseqOATIJL6EqSAkZ9 =Xnie -----END PGP SIGNATURE-----
--- End Message ---
