[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build
Obenchain, Valerie
Valerie.Obenchain at roswellpark.org
Thu Dec 17 17:47:23 CET 2015
Thanks!
Valerie
On 12/17/2015 08:32 AM, Brad Friedman wrote:
> Thanks, I've made the corresponding change to release version, and
> bumped minor version there.
>
> I previously only made it to devel.
>
> Brad
>
> On Thu, Dec 17, 2015 at 8:21 AM, Obenchain, Valerie
> <Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at roswellpark.org>> wrote:
>
> Hi Brad,
>
> Following up on this because AnalysisPageServer is still broken in
> release. Can you please fix?
>
> Thanks.
> Valerie
>
>
> On 12/14/2015 01:36 PM, Morgan, Martin wrote:
> > At least for the R package side of things, I think the question
> of how to invoke R CMD in a Makefile is moot for
> AnalysisPageServer -- remove the Makefile, and the shared object
> is created automatically when the package is built with R CMD
> build AnalysisPageServer.
> >
> > But for the record the format for referring to R in Writing R
> Extensions in a Makefile is
> >
> > "${R_HOME}/bin/R" ...
> >
> > ${R_HOME} is an environment variable, quotes allow for spaces in
> the path. A more cross-platform version is I think
> >
> > "${R_HOME}/bin${R_ARCH_BIN}/R"
> >
> > where on single-architecture platforms ${R_ARCH_BIN} is
> undefined hence harmless.
> >
> > Somewhat circularly, R_HOME is set by R CMD
> >
> > $ env|grep R_HOME
> > $ R CMD env|grep R_HOME
> > R_HOME=/home/mtmorgan/bin/R-devel
> > $ Rrel CMD env|grep R_HOME
> > R_HOME=/home/mtmorgan/bin/R-3-2-branch
> >
> > ________________________________________
> > From: Bioc-devel [bioc-devel-bounces at r-project.org
> <mailto:bioc-devel-bounces at r-project.org>] on behalf of Dan
> Tenenbaum [dtenenba at fredhutch.org <mailto:dtenenba at fredhutch.org>]
> > Sent: Monday, December 14, 2015 4:06 PM
> > To: Brad Friedman
> > Cc: bioc-devel
> > Subject: Re: [Bioc-devel] R CMD SHLIB throwing error on zin1
> (linux) BioC nightly build
> >
> > ----- Original Message -----
> >> From: "Brad Friedman" <friedman.brad at gene.com
> <mailto:friedman.brad at gene.com>>
> >> To: "bioc-devel" <bioc-devel at r-project.org
> <mailto:bioc-devel at r-project.org>>
> >> Sent: Monday, December 14, 2015 1:01:24 PM
> >> Subject: [Bioc-devel] R CMD SHLIB throwing error on zin1
> (linux) BioC nightly build
> >> I’m getting an error that R cannot be found on the nightly
> build server.
> >> Obviously it can be found at some point, since R CMD build
> started, but at
> >> the moment of calling R CMD SHLIB it can’t be found again.
> >>
> >> I was wondering if anything had changed on the server, or maybe
> I’m doing
> >> my Makefile wrong.
> >
> > Probably both. We made a change, removing R from the PATH on the
> linux and windows machines (on Mac R is in /usr/bin so it's a bad
> idea to remove that directory from the PATH) because we realized
> that there are packages that fail when R is not in the PATH, and
> one can't assume that R will always be in the path, so we wanted
> to make sure those packages failed so that we'd find the problems.
> That seems to be what is happening in your case.
> >
> > I'm not sure what the exact syntax is, but your makefile should
> reference R as $R_HOME/bin/R.
> >
> > Dan
> >
> >
> >> The error only happens on the linux server: mac (oaxaca)
> >> and windows (moscato1) build fine. And I can’t reproduce this
> on my local
> >> linux server with a fresh checkout.
> >>
> >> Nightly build
> >>
> <http://bioconductor.org/checkResults/release/bioc-LATEST/AnalysisPageServer/zin1-buildsrc.html>
> >> results:
> >>
> >>
> ##############################################################################
> >>
> ##############################################################################
> >> ###
> >> ### Running command:
> >> ###
> >> ### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD build
> --keep-empty-dirs
> >> --no-resave-data AnalysisPageServer
> >> ###
> >>
> ##############################################################################
> >>
> ##############################################################################
> >>
> >> * checking for file ‘AnalysisPageServer/DESCRIPTION’ ... OK
> >> * preparing ‘AnalysisPageServer’:
> >> * checking DESCRIPTION meta-information ... OK
> >> * cleaning src
> >> * installing the package to build vignettes
> >> -----------------------------------
> >> * installing *source* package ‘AnalysisPageServer’ ...
> >> ** libs
> >> ** arch -
> >> R CMD SHLIB AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp catch.c
> >> SearchReplace2.cpp R_init_AnalysisPageServer.cpp -o
> >> AnalysisPageServer.so
> >> /bin/bash: R: command not found
> >> make: *** [AnalysisPageServer] Error 127
> >> ERROR: compilation failed for package ‘AnalysisPageServer’
> >> * removing ‘/tmp/RtmpREgK1P/Rinst3e5828c9cd0f/AnalysisPageServer’
> >> -----------------------------------
> >> ERROR: package installation failed
> >>
> >> and the contents of src/Makefile:
> >>
> >> AnalysisPageServer: AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp
> >> AnalysisPageSVG.h tinyxml2.h cor.h catch.c SearchReplace2.cpp
> >> SearchReplace2.h catch.h
> >> R CMD SHLIB AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp catch.c
> >> SearchReplace2.cpp R_init_AnalysisPageServer.cpp -o
> >> AnalysisPageServer.so
> >> clean:
> >> rm *.o *.so
> >>
> >>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> mailing list
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