Your message dated Tue, 26 Jan 2021 08:21:54 +0000 with message-id <e1l4jbm-0004up...@fasolo.debian.org> and subject line Bug#980740: fixed in r-bioc-geoquery 2.58.0+dfsg-2 has caused the Debian Bug report #980740, regarding r-bioc-geoquery: flaky autopkgtests failing to download test data 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.) -- 980740: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980740 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: r-bioc-geoquery Version: 2.58.0+dfsg-1 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: flaky Hi Maintainer The autopkgtests of r-bioc-geoquery seem to download large amounts of test data from the internet, and these downloads often fail [1]. This makes the autopkgtests unsuitable for regression testing. I've copied parts of some recent failing logs below. Regards Graham [1] https://ci.debian.net/packages/r/r-bioc-geoquery/testing/arm64/ trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz' Content type 'application/x-gzip' length 5733793 bytes (5.5 MB) ================================================== downloaded 5.5 MB ── 1. Error: case-mismatched IDs in GSEs handled correctly (@test_GSE.R#15) ─── download from 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full' failed Backtrace: 1. GEOquery::getGEO("GSE35683") 2. GEOquery:::getAndParseGSEMatrices(...) 3. GEOquery:::parseGSEMatrix(...) 4. GEOquery::getGEO(GPL, AnnotGPL = AnnotGPL, destdir = destdir) 5. GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 6. utils::download.file(...) ... trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34145/matrix/GSE34145-GPL6102_series_matrix.txt.gz' Content type 'application/x-gzip' length 1428433 bytes (1.4 MB) ================================================== downloaded 1.4 MB ── 1. Error: short GSE handled correctly (@test_GSE.R#28) ───────────────────── cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6102&form=text&view=full' Backtrace: 1. GEOquery::getGEO("GSE34145") 2. GEOquery:::getAndParseGSEMatrices(...) 3. GEOquery:::parseGSEMatrix(...) 4. GEOquery::getGEO(GPL, AnnotGPL = AnnotGPL, destdir = destdir) 5. GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 6. utils::download.file(...) ... trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz' Content type 'application/x-gzip' length 8480960 bytes (8.1 MB) downloaded 0 bytes ── 1. Error: GSE without GPL works (@test_fetch_GPL_false.R#5) ──────────────── download from 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz' failed Backtrace: 1. GEOquery::getGEO("GSE2553", getGPL = FALSE) 2. GEOquery:::getAndParseGSEMatrices(...) 3. utils::download.file(...) ... trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz' Content type 'application/x-gzip' length 8480960 bytes (8.1 MB) ================================================== downloaded 8.1 MB ── 1. Error: generic GPL parsing works as expected (@test_GPL.R#5) ──────────── download from 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&view=full' failed Backtrace: 1. GEOquery::getGEO("GPL96") 2. GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL) 3. utils::download.file(...) ... trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz' Content type 'application/x-gzip' length 5733793 bytes (5.5 MB) downloaded 0 bytes ── 2. Error: case-mismatched IDs in GSEs handled correctly (@test_GSE.R#15) ─── download from 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE35nnn/GSE35683/matrix/GSE35683_series_matrix.txt.gz' failed Backtrace: 1. GEOquery::getGEO("GSE35683") 2. GEOquery:::getAndParseGSEMatrices(...) 3. utils::download.file(...)
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--- Begin Message ---Source: r-bioc-geoquery Source-Version: 2.58.0+dfsg-2 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of r-bioc-geoquery, 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 980...@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-geoquery 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: Tue, 26 Jan 2021 08:35:51 +0100 Source: r-bioc-geoquery Architecture: source Version: 2.58.0+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: 980740 Changes: r-bioc-geoquery (2.58.0+dfsg-2) unstable; urgency=medium . * Team upload. * Skip flaky test which are loading large amounts of data Closes: #980740 * Standards-Version: 4.5.1 (routine-update) Checksums-Sha1: f78d28ad78dcef613f950e05b71511c50ae33f63 2281 r-bioc-geoquery_2.58.0+dfsg-2.dsc 73c65f0decc85ffe36b6a40eba035c4ac25dc577 2864 r-bioc-geoquery_2.58.0+dfsg-2.debian.tar.xz a2f371064d934d604be87e50c9d79005a902d808 11516 r-bioc-geoquery_2.58.0+dfsg-2_amd64.buildinfo Checksums-Sha256: b3f9c1c6ee576b86562bf48f77c68ce9908fdbecbbb27d9dd2ce9b5d5beb0a64 2281 r-bioc-geoquery_2.58.0+dfsg-2.dsc c4992ae9cf9369eca0927d35d5c6e3c00388e6a2fb18cdee0d2d3f37785dda4c 2864 r-bioc-geoquery_2.58.0+dfsg-2.debian.tar.xz 6859c90e6cc874d759ef8e2cb917d97e91c5696234ae963ff7b4cf90455d17f9 11516 r-bioc-geoquery_2.58.0+dfsg-2_amd64.buildinfo Files: 28d22b1a48d138d41509ee99cc9ada0d 2281 gnu-r optional r-bioc-geoquery_2.58.0+dfsg-2.dsc ed8e117ea592eaa5b135c2bacf0642c0 2864 gnu-r optional r-bioc-geoquery_2.58.0+dfsg-2.debian.tar.xz d0ce9c650276283de41d8fa541061148 11516 gnu-r optional r-bioc-geoquery_2.58.0+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmAPxyURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEYxg//St9+wr9ISF8NGlacV9Jk/5bz6FkH/1g9 sbRY2vLFxnnTtqeOKvhdD03rEtCNYV2EaLfo58KVT8/yag8xSQn8lLWbK6H9Vh1F LCtCaYTe5Vl+btZ+LF5ctrsX5Rq/2GxRUJh03LKrXNc2F1xl6FU3LXEDjTYrzrMd yT1X2onAO9HeyarxQixSQ7f7+tIpNNFlYgwhLoHfw0694NoQelMwKy6j/XbwPgTi NexR2XZ8ft27MG0dRFyH7SfHt716ZY5I1NLvo9ayO8fqZC65j0d2MZostgJFV8Zy l0OBbM1w0PGJ2glwoHPF+atXbJXeCVQWLolekwFAVTDn9FW1A9CftCpYy+5AMbOy 5gP3wwhKMRV6etTs5k+odAIxzOeAKcs6Yc/AiGgmrFAyNJwJrJ0DY5X443qWfghr n2n56cZdtq3EMAf4eodmrBuPEXvEi5VmU6UE4uTpOONKOA2S8WSOlPFsbETCxX1U p8KyhLAAxrGDrSrlSFnsK+LE8PhmrbFgpk+nXQWgTZRhvmgPAYvfaB+9K6TmamLm JPSKUGswXOI3OZEq3C5hy/Xd79hkSCB0e96kg04bk28gQMawGJ3XNvRjfLisEJ23 oup6sYYvf/Z8SwYCDIvfVse7u739hTUQvBVzCXmnm7Q3Icva5/Nh4Ge3Z5sTj2MK 5hvzzmW2DYo= =t7TQ -----END PGP SIGNATURE-----
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