Your message dated Fri, 19 Feb 2021 08:48:34 +0000 with message-id <e1ld1sk-0005xg...@fasolo.debian.org> and subject line Bug#983027: fixed in r-bioc-mutationalpatterns 3.0.1+dfsg-2 has caused the Debian Bug report #983027, regarding r-bioc-mutationalpatterns: autopkgtest regression in testing: no package called ‘BSgenome.Hsapiens.UCSC.hg19’ 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.) -- 983027: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=983027 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: r-bioc-mutationalpatterns Version: 2.0.0-2 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression Dear maintainer(s), With a recent (October 2020) change somewhere outside of your package the autopkgtest of your package started to fail. I copied some of the output at the bottom of this report. Can you please investigate the situation and fix it? More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-mutationalpatterns/10546520/log.gz ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error (test-bin_mutation_density.R:11:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-bin_mutation_density.R:11:0 ── Error (test-calculate_lesion_segretation.R:5:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-calculate_lesion_segretation.R:5:0 ── Error (test-context_potential_damage_analysis.R:13:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-context_potential_damage_analysis.R:13:0 ── Error (test-extract_signatures.R:19:1): (code run outside of `test_that()`) ── Error: Package 'ccfindR' is needed for variational_bayes to work. Please either install it or use the regular NMF. Backtrace: █ 1. └─MutationalPatterns::extract_signatures(...) test-extract_signatures.R:19:0 ── Error (test-get_indel_context.R:10:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-get_indel_context.R:10:0 ── Error (test-mut_context.R:10:1): (code run outside of `test_that()`) ──────── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-mut_context.R:10:0 ── Error (test-mut_matrix_stranded.R:6:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-mut_matrix_stranded.R:6:0 ── Error (test-mut_matrix.R:5:1): (code run outside of `test_that()`) ────────── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-mut_matrix.R:5:0 ── Error (test-mut_type_occurrences.R:10:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-mut_type_occurrences.R:10:0 ── Error (test-plot_spectrum_region.R:10:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-plot_spectrum_region.R:10:0 ── Error (test-plot_spectrum.R:11:1): (code run outside of `test_that()`) ────── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-plot_spectrum.R:11:0 ── Error (test-plot_strand.R:10:1): (code run outside of `test_that()`) ──────── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-plot_strand.R:10:0 ── Error (test-read_vcfs_as_granges.R:5:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-read_vcfs_as_granges.R:5:0 ── Error (test-strand_occurrences.R:10:1): (code run outside of `test_that()`) ── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-strand_occurrences.R:10:0 ── Error (test-type_context.R:10:1): (code run outside of `test_that()`) ─────── Error: there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’ Backtrace: █ 1. └─base::library(ref_genome, character.only = TRUE) test-type_context.R:10:0 [ FAIL 15 | WARN 0 | SKIP 0 | PASS 264 ]
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--- Begin Message ---Source: r-bioc-mutationalpatterns Source-Version: 3.0.1+dfsg-2 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of r-bioc-mutationalpatterns, 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 983...@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-mutationalpatterns 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, 18 Feb 2021 21:47:47 +0100 Source: r-bioc-mutationalpatterns Architecture: source Version: 3.0.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net> Changed-By: Andreas Tille <ti...@debian.org> Closes: 983027 Changes: r-bioc-mutationalpatterns (3.0.1+dfsg-2) unstable; urgency=medium . * Add hook to deal with unavailable BioC packages in test Closes: #983027 Checksums-Sha1: 49b880cda87e8ab839adf54d9fb35dd60950570d 2731 r-bioc-mutationalpatterns_3.0.1+dfsg-2.dsc 9eeb8bc77f640d78f39fe2f66645de3e2438626d 2952 r-bioc-mutationalpatterns_3.0.1+dfsg-2.debian.tar.xz 75ab40fc2cff9d8833509a3569a8f9fa559a1690 14538 r-bioc-mutationalpatterns_3.0.1+dfsg-2_amd64.buildinfo Checksums-Sha256: 4f40048ca8e22b0e79e5b3e089e4d31efa3f9b44aede357511c17e45ee5e2444 2731 r-bioc-mutationalpatterns_3.0.1+dfsg-2.dsc 243f360993c05ca9cd963f9d58ebcb63e1a7c1029f7050ea5e6dd5c011ca3e48 2952 r-bioc-mutationalpatterns_3.0.1+dfsg-2.debian.tar.xz aec58d08d2ac9a3fed481ca45075a9bc063bb023d0fde6c3897db6969244f65b 14538 r-bioc-mutationalpatterns_3.0.1+dfsg-2_amd64.buildinfo Files: 77e40a99137893e9822f3b110096f606 2731 gnu-r optional r-bioc-mutationalpatterns_3.0.1+dfsg-2.dsc c2395583c4fd2e4b08004b5d6f54fcce 2952 gnu-r optional r-bioc-mutationalpatterns_3.0.1+dfsg-2.debian.tar.xz a49b52419d8c0480641573182e6473a7 14538 gnu-r optional r-bioc-mutationalpatterns_3.0.1+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmAvdZARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF/eQ//VZjblwbG1jcBpXvKraSBWEX73omKrRyD jZICB1qm3uEs3YkVgaPntaEhr14NNKlRrI4Jox4P5tyr4VWIux/ykzqg1ruRvOAp lxpFGs0i/MdtYpJ4onC2Hwht7Ynk+t4WQv1oo1fjLdsnCYrwTnVuvCQimAAFdeW5 BRiGQfJFgTAWMed0uc/04X55TpNOTZWEBuAeYeOzZbJepL06wnRegTkpzFmCPM15 3xyW2UBnjAqTpKiFDWpf8moUmMXrJY8V0KHqYJAbjYgsrCnI3PIYml6+fJdENJiu IR7+wvlribJNHgEGSfRHOGFhc13KL3A78TEsKS1mTxt41TtJpQQeIWL4bMWUJbeW sLm+U+98qzPxnz0tjtTpwvNX4jG9xLcu8Fj6qzTGfw4QKXDHaETygxmosV3G0F0C mZsQZOchvnvNWsG0shnuBEYUNTQY/ZVP1kSm96P4z+sadc0GYcrk+6gUPiNePD35 PLv6a8opAx5MT7B5nj1fsKliE7as2s9M6rUyXC3B/6zyCp0GXIBKcXa/b1kbQTxa a2lnQOlBS+8u7zISdOj1KOeECuRFFIpppC0ntuoZIGq4cnXdMxw3zWdAysPoMJhx Szzy/Jyr+BBoloiowWUDMpLqk8pb4RSBJrdpJSlmepQNm7Zn9tTB8GtUIlGelS5+ JLYuyjJboxU= =AFws -----END PGP SIGNATURE-----
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