[Bioc-devel] Some build system news

Herve Pages hpages at fhcrc.org
Mon Dec 18 19:55:54 CET 2006

Kasper Daniel Hansen wrote:
> On Dec 15, 2006, at 4:28 AM, Herve Pages wrote:
>> "Main" build machine means that a devel package is made publicly
>> available
>> (by being pushed to http://bioconductor.org/packages/2.0/bioc/) only
>> if it
>> passes the CHECK on 'lamb1' with no error (it can have warnings though).
> I assume you have thought this through. I just want to point out the the
> lamb1 system is one specific architecture and there may be (development)
> packages that have problems only for specific architectures. This is of
> course mostly relevant for non-R code, and I may be a bit biased since I
> have worked on two packages where the platform differences really mattered.

Hi Kasper,

I should have said:

  "Main" build machine means that the _src_ tarball (.tar.gz) of a package is
   made publicly available if it passes the CHECK on 'lamb1' with no error.

For binary packages things are a little bit different:
  - lemming is our "main" Windows build machine
  - We don't build Mac binaries: we only build and check the source packages
    on derby, our Mac build machine. Universal binaries are built externally by
    Simon Urbanek (results are here http://r.research.att.com/reports/) but for
    release packages only.

I agree that the lamb1 system is still one specific platform among
many other Unix/Linux platforms. The underlying question is: on how many
platforms should a source package build and pass check before it can be
considered good enough to be made publicly available? And what is the exact
definition of "platform" to start with: is it just the microprossesor type
or the n-uplet (microprossesor type, OS type, OS version, compilers, etc...)?


> Kasper
>> Also, maybe you've been wondering what's going on with some package
>> description
>> pages:
>>   http://bioconductor.org/packages/2.0/bioc/
>> As you can see, the individual pages for the packages listed below the
>> GGtools
>> package are missing. This problem is related to the migration of all our
>> scripts from gopher5 to lamb1 and should get back to a normal state
>> tomorrow
>> around noon.
>> Also the build results for our new Windows server (liverpool) are
>> not looking good for an obscure pdflatex.exe error that occurs
>> when building most of the vignettes. We'll investigate this and
>> try to fix ASAP. In the meantime, if someone has already seen this
>> problem
>> before and can provide some usefull feedback, s/he is more than welcome.
>> A typical example can be seen here:
>> http://bioconductor.org/checkResults/2.0/liverpool-ABarray-buildsrc.html
>> Thanks!
>> Best,
>> H.
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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