[R-pkg-team] Bug#972137: r-bioc-tcgabiolinks: autopkgtest regression

[Graham Inggs]

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)