Bug#961591: Bug#961592: r-bioc-gviz: autopkgtest regression

[Andreas Tille]

On Wed, May 27, 2020 at 11:22:34AM +0200, Dylan Aïssi wrote:
> 
> But, regarding https://bugs.debian.org/961591 , I have no idea how to fix it.

I have no idea either.  What about seeking help at upstream?

Kind regards

  Andreas.

-- 
http://fam-tille.de

Bug#961592: r-bioc-gviz: autopkgtest regression

[Dylan Aïssi]

Hi,

Le mer. 27 mai 2020 à 11:12, Andreas Tille  a écrit :
>
> Ahhh, its new to me that pkg-r-autopkgtest does more than just
> loading the library.  Hmmm, Dylan, do you have any idea besides
> patching the test suite?
>

I am testing my patch that skip the test if
"BSgenome.Hsapiens.UCSC.hg19" is not available, so this bug should be
fixed soon.

But, regarding https://bugs.debian.org/961591 , I have no idea how to fix it.

Best,
Dylan

Bug#961592: r-bioc-gviz: autopkgtest regression

[Andreas Tille]

Hi Graham,

On Wed, May 27, 2020 at 11:13:07AM +0200, Graham Inggs wrote:
> 
> Note this is not run-unit-test, this is pkg-r-autopkgtest.

Ahhh, its new to me that pkg-r-autopkgtest does more than just
loading the library.  Hmmm, Dylan, do you have any idea besides
patching the test suite?

Kind regards

 Andreas.

-- 
http://fam-tille.de

Bug#961592: r-bioc-gviz: autopkgtest regression

[Graham Inggs]

Hi Andreas

On Wed, 27 May 2020 at 10:55, Andreas Tille  wrote:
> That's strange.  The autopkgtest should not run.  r-bioc-gviz source
> has
>
> debian/tests/control_unused
>
> to deactivate its test.  Has anything changed in debci that fetches
> anything that looks like a test script?

Note this is not run-unit-test, this is pkg-r-autopkgtest.

Regards
Graham

Bug#961592: r-bioc-gviz: autopkgtest regression

[Andreas Tille]

Hi Graham,

On Tue, May 26, 2020 at 02:37:04PM +0200, Graham Inggs wrote:
> Since the upload of 1.32.0+dfsg-1, r-bioc-gviz has been failing its
> own autopkgtests [1].   This now prevents the migration of r-base.
> I've copied what I hope is the relevant part of the log below.

That's strange.  The autopkgtest should not run.  r-bioc-gviz source
has

debian/tests/control_unused

to deactivate its test.  Has anything changed in debci that fetches
anything that looks like a test script?

Kind regards

 Andreas.

-- 
http://fam-tille.de

Bug#961592: r-bioc-gviz: autopkgtest regression

[Graham Inggs]

Source: r-bioc-gviz
Version: 1.32.0+dfsg-1
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: regression

Hi Maintainer

Since the upload of 1.32.0+dfsg-1, r-bioc-gviz has been failing its
own autopkgtests [1].   This now prevents the migration of r-base.
I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/r/r-bioc-gviz/unstable/amd64/


> test_check("Gviz")
Error in library(BSgenome.Hsapiens.UCSC.hg19) :
  there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
Execution halted
autopkgtest [15:02:19]: test pkg-r-autopkgtest: ---]
autopkgtest [15:02:19]: test pkg-r-autopkgtest:  - - - - - - - - - -
results - - - - - - - - - -
pkg-r-autopkgtestFAIL non-zero exit status 1