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List: bioc-devel
Subject: Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build
From: Brad Friedman <friedman.brad () gene ! com>
Date: 2015-12-17 16:58:57
Message-ID: 797280A7-A7E6-4B71-8DB7-9361EAD21EE9 () gene ! com
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Thank YOU!!! Bioconductor is fantastic.
Brad Friedman
617-230-7055
> On Dec 17, 2015, at 8:47 AM, "Obenchain, Valerie" \
> <Valerie.Obenchain@RoswellPark.org> wrote:
> 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@roswellpark.org
> > <mailto:Valerie.Obenchain@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@r-project.org
> > <mailto:bioc-devel-bounces@r-project.org>] on behalf of Dan
> > Tenenbaum [dtenenba@fredhutch.org <mailto:dtenenba@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@gene.com
> > <mailto:friedman.brad@gene.com>>
> > > > To: "bioc-devel" <bioc-devel@r-project.org
> > <mailto:bioc-devel@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@r-project.org <mailto:Bioc-devel@r-project.org>
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> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
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> This email message may contain legally privileged and/or confidential information. \
> If you are not the intended recipient(s), or the employee or agent responsible for \
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