Hello
I had a look at which packages are have long-term test failures on
debian CI [1]. This list doesn't include failures only on arm64, or
those for which the tests have recently passed and are perhaps random
failures.
At least half of the failing packages appear to fail for trivial and
hopeful
[Jonathon, please seek for your name in the text below.]
Hi Gordon,
thanks a lot for your effort about testing R packages.
On Wed, Apr 27, 2016 at 12:00:05PM +0200, Gordon Ball wrote:
>
> non-lowercased path for vignette: output contains something like "cannot
> stat /usr/share/doc/r-bioc-biovi
hi andreas,
i've pushed fixes to:
- r-cran-bms
- r-cran-contfrac
- r-cran-hypergeo (new upstream actually)
thanks for pointing these out.
i do receive a `hardening-no-bindnow` on r-cran-contfrac, but i can't
figure out how to add arguments to the linker from the R Makevars file
(i think
On Thu, Apr 28, 2016 at 01:38:54PM +1000, Jonathon Love wrote:
> hi andreas,
>
> i've pushed fixes to:
>
> - r-cran-bms
Did you really push?
r-cran-bms(master) $ git log
commit 4de85fa06d10e6aa3181b63efd35e70239fff861
Author: Jonathon Love
Date: Sat Dec 19 14:48:39 2015 +1100
Updated
i've pushed fixes to:
- r-cran-bms
Did you really push?
my bad. pushed now.
i do receive a `hardening-no-bindnow` on r-cran-contfrac, but i can't figure
out how to add arguments to the linker from the R Makevars file (i think it
is necessary to patch Makevars).
the following doesn't work:
Continued my previous mail:
> r-cran-sp: missing dep rgeos (unpackaged?)
As far as I can see rgeos is not yet packaged. Any volunteer?
Otherwise tweaking the tests requiring this package might be an
intermediate solution.
> r-cran-surveillance: unsatisfyable dependencies
New upstream version u
On 28/04/16 00:22, Andreas Tille wrote:
> [Jonathon, please seek for your name in the text below.]
>
> Hi Gordon,
>
> thanks a lot for your effort about testing R packages.
>
> On Wed, Apr 27, 2016 at 12:00:05PM +0200, Gordon Ball wrote:
>>
>> non-lowercased path for vignette: output contains so
On Thu, Apr 28, 2016 at 10:42:45AM +0200, Gordon Ball wrote:
> > me. My only idea is to rather use
> >
> >pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
> >
> > and so I try this even if I think this is equivalent.
>
> Hmm, yes. I can't obviously see why this fails. (Aside - `tr A-Z a-z`
> w
More fixes below:
On Thu, Apr 28, 2016 at 12:22:22AM +0200, Andreas Tille wrote:
> My only idea is to rather use
>
>pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
>
> and so I try this even if I think this is equivalent.
This seems to work.
> > r-bioc-aroma.light: attempts install.packages
>> However, since the working dir for the test is the root of the
extracted
>> source package, we should be able to extract the R and debian package
>> names directly rather than hardcoding or deriving them:
>>
>> rpkg=$(grep-dctrl -s Package -n '' DESCRIPTION)
>> dpkg=$(grep-dctrl -s Pac
Hi Gordon,
On Fri, Apr 29, 2016 at 01:29:50PM +0200, Gordon Ball wrote:
> > I confirm that if you use the script for CI *only* this would work
> > nicely. However, I consider it a good idea to provide the user with
> > some test case / example use and thus I always put the script into
> > /usr/sh
Having had a better look at some of the less obvious failings:
r-bioc-biocparallel
---
Non-deterministic? Seems to fail about 80% of the time in
test_bpaggregate.R when calling
bpworkers(param) <- 2
This is the only call to bpworkers() in the test suite, but I can't
obviousl
Hi Gordon,
thanks for your investigation.
On Tue, May 03, 2016 at 04:05:22PM +0200, Gordon Ball wrote:
> Having had a better look at some of the less obvious failings:
>
> r-bioc-biocparallel
> ---
>
> Non-deterministic? Seems to fail about 80% of the time in
> test_bpaggregate.
On 3 May 2016 at 22:53, Andreas Tille wrote:
| If we do not receive any hint from upstream removing this test seems to
[...]
| Hoping for upstream to respond to my first mail. I might ping at
[...]
| I might ping upstream.
[...]
They won't know what you are talking about, and for a reason. The
I don't have permissions for debian-med, nor am I a DM/DD, so I'm afraid
I haven't committed any patches or uploaded them, but a couple should be
attached here.
>> r-bioc-biomart
>> --
>>
>> The test suite never succeeds, but fails at apparently random points
>> with malformed XML erro
On Fri, May 13, 2016 at 05:37:35PM +0200, Gordon Ball wrote:
> I don't have permissions for debian-med, nor am I a DM/DD, so I'm afraid
> I haven't committed any patches or uploaded them, but a couple should be
> attached here.
In any case I've added you to the Debian Med team to enable you
commit
On Sat, May 14, 2016 at 03:56:40PM +0200, Andreas Tille wrote:
> >
> > Patch (git format-patch for the repository) is attached. It
> > suppress_test_writing_to_usr.patch, which removed some of the pre-amble
> > to each vignette with one which modifies the paths the vignettes check
> > for their da
Returning a few weeks later: CRAN packages.
r-cran-adegraphics:
r-cran-surveillance:
waiting for r-cran-spdep
r-cran-afex:
run-unit-test script hides output, so you don't see what goes wrong
missing test dependency on r-cran-dplyr
missing test dependency on mlmrev (not packaged) for the "conce
Hi,
On Wed, Jun 08, 2016 at 03:50:18PM +0200, Gordon Ball wrote:
> Returning a few weeks later: CRAN packages.
>
> r-cran-adegraphics:
> r-cran-surveillance:
>
> waiting for r-cran-spdep
Its the fourth time in new queue and I tried to convince ftpmaster
that it is urgend (with no success for th
Hi again,
On Wed, Jun 08, 2016 at 05:05:15PM +0200, Andreas Tille wrote:
> > Returning a few weeks later: CRAN packages.
> >
> > r-cran-adegraphics:
> > r-cran-surveillance:
> >
> > waiting for r-cran-spdep
>
> Its the fourth time in new queue and I tried to convince ftpmaster
> that it is urge
On Thu, Jun 09, 2016 at 03:07:35PM +0200, Andreas Tille wrote:
> > > missing test dependency on mlmrev (not packaged) for the "conception"
> > > dataset
> >
> > Any volunteer for mlmrev?
>
> ITPed and in SVN, will upload today to new. Both packages are added as
> test Depends.
Its really upload
On 09/06/16 15:07, Andreas Tille wrote:
> Hi again,
>
> On Wed, Jun 08, 2016 at 05:05:15PM +0200, Andreas Tille wrote:
>>> Returning a few weeks later: CRAN packages.
>>>
>>> r-cran-adegraphics:
>>> r-cran-surveillance:
>>>
>>> waiting for r-cran-spdep
>>
>> Its the fourth time in new queue and I
Pushed some fixes to git/svn:
* r-cran-doparallel: extra test dependency r-cran-rpart, patch which
removes an attempt to write a report within the (read-only) package dir
* r-cran-matrixstats: cp and rm in run-unit-test didn't work with subdirs
* r-cran-mlmrev: wrong package name in run-unit-te
On Fri, Jun 17, 2016 at 04:18:40PM +0200, Gordon Ball wrote:
> Pushed some fixes to git/svn:
>
> * r-cran-doparallel: extra test dependency r-cran-rpart, patch which
> removes an attempt to write a report within the (read-only) package dir
Uploaded.
> * r-cran-matrixstats: cp and rm in run-uni
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