[Bioc-devel] new package build problems

[Dan Tenenbaum]

----- Original Message -----
> From: "Karl Stamm" <karl.stamm at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Tuesday, September 30, 2014 3:45:37 PM
> Subject: Re: [Bioc-devel] new package build problems
> 
> 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:
> http://bioconductor.org/spb_reports/rgsepd_0.99.3_buildreport_20140930152650.html#oaxaca_check_anchor
> 
> 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!
> 

This is an internal problem with the build system, you can disregard it. Hopefully it will disappear soon.
It's not a problem with your package.

Dan


> Thanks again.
> 
> 
> 
> On Tue, Sep 30, 2014 at 2:46 AM, Sander Bollen
> <sander.h.bollen at gmail.com>
> wrote:
> 
> > 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
> >>  ERROR
> >> 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
> >>
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
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