[Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

[Kasper Daniel Hansen]

Giula,

Provided your package has been accepted by a reviewer, it will be released
as part of Bioconductor 3.12, as long as it satisfies the other
requirements, which includes some deadlines for when it is supposed to pass
check without errors.

In general, around release, there are a lot of changes to a lot of
packages. When you get an error from the build system, I suggest looking
closely at the error and also see if other packages are affected.
Unfortunately, sometimes things break on the build system which leads to
100s or 1000s of packages failing at the same time. For this reason, it is
sometimes useful to look at the Dashboard:
  http://www.bioconductor.org/dashboard/
Today you can see ~20 packages failing build, ~70 failing installation and
~70 failing check (rough numbers across platforms). Nothing seems to be
amiss with windows.

Today you have a warning on one windows platform which suggests there is
something wrong with IRanges on that platform,

If you see occasional failures (errors), there could be many reasons
including internet access, memory overflow and failure to write to disk.
Its hard to know what you're suffering from without knowing your package.

On Sun, Oct 25, 2020 at 9:57 PM Giulia Pais <giuliapais1 using gmail.com> wrote:

> Hello,
>
> we keep getting weird warning messages for check on windows, it's also
> even more odd since we got yesterday a build report with no errors or
> warnings but the build report for today gives an error on Windows Server
> 2012 R2 Standard / x64 only. We can't understand what the warning is,
> why does it happen only for tests and also why it doesn't happen
> consistently (same lines of codes are run in examples in the
> documentation).
>
> Could you give us further insight on the meaning of this warning? We are
> not able to reproduce it.
>
> Also will our package be released for bioconductor 3.12?
>
> Thank you
>
> Il 21/10/2020 19:08, Pages, Herve ha scritto:
> > Hi Giulia,
> >
> > Today's report is available. Unfortunately ISAnalytics tests are still
> > failing on Windows:
> >
> >
> >
> https://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/tokay1-checksrc.html
> >
> > Note that you have this warning at the beginning of the tests:
> >
> >     > test_check("ISAnalytics")
> >     Warning message:
> >     In file(file, "rt") :
> >       file("") only supports open = "w+" and open = "w+b": using the
> former
> >
> > Maybe it's relevant?
> >
> > In any case, that warning should not be ignored as it is most likely
> > reporting a real problem.
> >
> > Best,
> > H.
> >
> >
> > On 10/21/20 02:58, Giulia Pais wrote:
> >> Hello, bioconductor team,
> >>
> >> I'm one of the contributors for the package ISAnalytics. We pushed some
> >> changes we would like to be included in the release for bioconductor
> >> 3.12 a couple of days ago but the build report still refers to the older
> >> version, did we miss the deadline for updates or is it normal? Moreover,
> >> by taking a look at the build report for the older version we noticed it
> >> had failed on Windows, which is to us very odd, since we develop and
> >> check the package on windows locally and we also have github automated
> >> actions that perform the same checks on other machines and there were no
> >> errors or warnings. From what we can see from the report it seems a
> >> BiocParallel problem, could you give us feedback on this please? The
> >> link to the build report:
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ISAnalytics_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=gGAt_tpoNlVhB63K8IusN9oxHe9SQzGi6T3Drsx4jxU&e=
> >>
> >> Thank you in advance,
> >>
> >> Giulia Pais
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CHJeB1qsdWS04WzhReQyXwYrMCo0ZFIzgm8KFXf0dSU&s=9yNBZH8vQVM9oEPd9kEepBSAQH0XcokumxvYXW_bYxA&e=
> >>
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

	[[alternative HTML version deleted]]