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

[Andreas Tille]

Hi Graham,

so what is you suggestion?  Simply droping the test is possibly
not the best solution.  Marking it flaky comes to mind.  What
do you think?

Kind regards

      Andreas.

On Thu, Jan 21, 2021 at 10:52:49AM +0200, Graham Inggs wrote:
> 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(...)
> 
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