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

[Tiago Chedraoui Silva]

Hi Andreas,

The software access an external database to retrieve the genome
information. The database has experienced problems in the last days and it
has not been fixed yet.

I am trying to save the genome information inside the package so it does
not depends on the database anymore. I'll let you know when I fix it.

Best regards,
Tiago Chedraoui Silva


On Tue, Oct 13, 2020 at 6:04 AM Andreas Tille <tille at debian.org> wrote:

> 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)
> >
> > _______________________________________________
> > R-pkg-team mailing list
> > R-pkg-team at alioth-lists.debian.net
> > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team
>
> --
> http://fam-tille.de
>
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