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(...)