[Bioc-devel] Build error: Dependency 'Biobase' is not available

[Shraddha Pai]

Hi Hervé,
Thank you for the feedback, that makes sense. Thanks also to all the BioC
system admins for maintaining such a large system of interdependent
packages. BioC makes complex genomics data analysis so easily accessible to
community researchers.

Regards,
Shraddha


On Wed, Oct 26, 2016 at 3:32 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Shraddha,
>
> On 10/26/2016 11:12 AM, Shraddha Pai wrote:
>
>> Hello BioC developers,
>>
>> I'm not sure why the nightly build of my package IdeoViz is reporting this
>> error on tokay (see message below). It seems to me that not having Biobase
>> installed is such a fundamental problem that the package should have been
>> flagged when it first got submitted (sometime in 2014). What am I missing?
>>
>
> If you look at the full report
>
>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/
>
> you'll see that hundreds of packages were victims of that problems
> during yesterday builds. This is a problem we see sometimes on the
> Windows builders. We're working on it.
>
> The problem should clear out in a couple of hours when the report
> gets updated with the results of today's builds.
>
> Sorry for the inconvenience.
>
>
>> Separately, I got a message about 10 days back reporting a build error on
>> malbec1, but that seems to have resolved without my intervention. Does
>> anyone know what the case could have been there?
>>
>
> Hard to know for sure without knowing the details of the build error but
> if your package is trying to access some remote resource then it could
> be that it failed 10 days ago because that resource was momentarily
> unavailable.
>
> Cheers,
> H.
>
>
>> ----
>>
>> * checking for file 'IdeoViz/DESCRIPTION' ... OK
>> * preparing 'IdeoViz':
>> * checking DESCRIPTION meta-information ... OK
>> * installing the package to build vignettes
>> Warning: running command
>> '"C:/Users/biocbuild/bbs-3.5-bioc/R/bin/x64/Rcmd.exe" INSTALL -l
>> "C:\Users\biocbuild\bbs-3.5-bioc\tmpdir\Rtmpu0feNb\Rinst1230396730de"
>> --no-multiarch "C:/Users/biocbuild/bbs-3.5-bi
>> oc/tmpdir/Rtmpu0feNb/Rbuild123010852598/IdeoViz"'
>> had status 1
>>       -----------------------------------
>> ERROR: dependency 'Biobase' is not available for package 'IdeoViz'
>> * removing 'C:/Users/biocbuild/bbs-3.5-bioc/tmpdir/Rtmpu0feNb/Rinst1230
>> 396730de/IdeoViz'
>>       -----------------------------------
>> ERROR: package installation failed
>>
>> ---
>>
>> Thanks for your time,
>> Shraddha
>> ----
>> Shraddha Pai
>> Post-doctoral Fellow, http://baderlab.org
>> The Donnelly Center, University of Toronto
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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