[Bioc-devel] new package build problems

Karl Stamm karl.stamm at gmail.com
Wed Oct 1 00:45:37 CEST 2014

Hello all, I'm running into some problems submitting my first bioconductor
package. Hope someone can help.

I've got the package building and checking successfully on three of the
four build servers, and a strange error on the last. The OSX *oaxaca* host
reports a warning during CHECK. Reviewing the log has this apparent error:

* checking loading without being on the library search path ... WARNING

Loading required package: DESeq

Loading required package: BiocGenerics

Loading required package: lattice

Error : Function found when exporting methods from the namespace IRanges
which is not S4 generic: unsplit

Error: package DESeq could not be loaded

Execution halted

It looks like this package has a loading problem when not on .libPaths:

see the messages for details.

* checking dependencies in R code ... OK

Later in the log it says

* checking examples ... [259s/264s] OK

Which tells me it must have loaded all required packages. Later, oaxaca's
BUILD bin successfully installs the package, which is more confusing. I
don't have an unsplit() and I don't use IRanges directly, those are
imported from BiocGenerics.

The full build report is here:

Sorry I have to lean on the mailing list for support, but when it builds
and checks successfully on 3/4 hosts, I'm stumped!

Thanks again.

On Tue, Sep 30, 2014 at 2:46 AM, Sander Bollen <sander.h.bollen at gmail.com>

> Hi there,
> I have had this issue as well when submitting my package. In my case it
> turned out that the Windows build apparently can't handle bibtex/biblatex
> very well. Looks like your build also stops at bibtex. If you have just a
> few references, you might just put them in the old-fashioned way (i.e. by
> hand).
> Kind regards,
> Sander Bollen.
> 2014-09-30 7:04 GMT+02:00 Karl Stamm <karl.stamm at gmail.com>:
>> I'm trying to put together a new package submission, "rgsepd", and I've
>> ran
>> into an error I can't figure out. Hoping to talk with someone with more
>> experience on the bioconductor build system.
>> The build report is here
>> http://bioconductor.org/spb_reports/rgsepd_0.99.2_buildreport_20140929213816.html#moscato1_buildsrc_anchor
>> The package has built fine on OSX and Linux, but is now crashing trying to
>> construct the Vignette on Windows. I don't see any error message reported,
>> just that the vignette failed. So I don't know how to debug it anymore.
>> Earlier versions had reported various file-not-found errors, so I could
>> track them down and fix them, it was file case-sensitivity or
>> forward-slash
>> vs backslash on various imported files.  On the latest revision 0.99.2,
>> the
>> moscato1 BUILD failed, but it was working in 0.99.1. I'm kind of at a
>> loss,
>> does moscato1 not like knitr ?
>> The content of the error log only says it didn't make the file, as far as
>> I
>> can tell:
>> * installing the package to build vignettes
>> * creating vignettes ...Warning: running command
>> '"D:/packagebuilder/R/bin/i386/Rscript" --vanilla --default-packages=
>> -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
>> Warning: running command
>> '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe" --quiet --pdf
>> "rgsepd.tex" --max-iterations=20 -I
>> "D:/packagebuilder/R/share/texmf/tex/latex" -I
>> "D:/packagebuilder/R/share/texmf/bibtex/bst"' had status 1
>> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
>>   Failed to locate the 'texi2pdf' output file (by engine
>> 'knitr::knitr') for vignette with name 'rgsepd'. The following files
>> exist in directory '.': 'rgsepd.R', 'rgsepd.Rnw', 'rgsepd.tex'
>> Calls: <Anonymous> -> find_vignette_product
>> Execution halted
>> Is there any way to get more information for debugging?
>> Thanks for your help.
>>         [[alternative HTML version deleted]]
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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