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.obench...@roswellpark.org > <mailto:valerie.obench...@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-boun...@r-project.org > <mailto:bioc-devel-boun...@r-project.org>] on behalf of Dan > Tenenbaum [dtene...@fredhutch.org <mailto:dtene...@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.b...@gene.com > <mailto:friedman.b...@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> > mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > This email message may contain legally privileged and/or > confidential information. 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