[R-pkg-team] Bug#980740: r-bioc-geoquery: flaky autopkgtests failing to download test data

[Graham Inggs]

Source: r-bioc-geoquery
Version: 2.58.0+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at 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(...)