[R-pkg-team] Bug#972137: SSL certificate problem (Was: Bug#972137: r-bioc-tcgabiolinks: autopkgtest regression)

[Andreas Tille]

Control: tags -1 upstream
Control: tags -1 help
Control: forwarded -1 Antonio Colaprico <axc1833 at med.miami.edu>, Tiago Chedraoui Silva <tiagochst at usp.br>


Hi Antonio and Tiago,

the Debian packaged version of TCGAbiolinks received a bug report about
a failure in its test suite.  I have the impression that the SSL
certificate of a site where data are downloaded from is not correct.
Could you please verify the test suite and let me know whether you
might also get

 ── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193)  ─                                                                                                           
 failed to get URL after 3 tries:                                                                                                                                                           
   error: SSL certificate problem: unable to get local issuer certificate                                                                                                                   

Kind regards

       Andreas.

On Tue, Oct 13, 2020 at 08:36:21AM +0200, Graham Inggs wrote:
> Source: r-bioc-tcgabiolinks
> Version: 2.16.4+dfsg-1
> Severity: serious
> Tags: sid bullseye
> X-Debbugs-CC: debian-ci at lists.debian.org
> User: debian-ci at lists.debian.org
> Usertags: regression
> 
> Hi Maintainer
> 
> Since 2020-10-08, the autopkgtest of r-bioc-tcgabiolinks has been failing [1].
> 
> I've copied what I hope is the relevant part of the log below.
> 
> Does this autopkgtest download data?  If so, please add the
> 'needs-internet' [2] restriction to debian/tests/control, or even skip
> that particular test.
> 
> Regards
> Graham
> 
> 
> [1] https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/amd64/
> [2] https://salsa.debian.org/ci-team/autopkgtest/raw/master/doc/README.package-tests.rst
> 
> 
> ── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193)  ─
> failed to get URL after 3 tries:
>   error: SSL certificate problem: unable to get local issuer certificate
> Backtrace:
>  1. TCGAbiolinks::GDCprepare(query, summarizedExperiment = TRUE)
>  2. TCGAbiolinks:::readGeneExpressionQuantification(...)
>  3. TCGAbiolinks:::makeSEfromGeneExpressionQuantification(...)
>  4. TCGAbiolinks::get.GRCh.bioMart(genome)
> 
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