Thank YOU!!! Bioconductor is fantastic. Brad Friedman 617-230-7055
> On Dec 17, 2015, at 8:47 AM, "Obenchain, Valerie" > <valerie.obench...@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.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. If you are not the intended >> recipient(s), or the employee or agent responsible for the >> delivery of this message to the intended recipient(s), you are >> hereby notified that any disclosure, copying, distribution, or use >> of this email message is prohibited. If you have received this >> message in error, please notify the sender immediately by e-mail >> and delete this email message from your computer. Thank you. >>> _______________________________________________ >>> 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. If you are not the intended >> recipient(s), or the employee or agent responsible for the >> delivery of this message to the intended recipient(s), you are >> hereby notified that any disclosure, copying, distribution, or use >> of this email message is prohibited. If you have received this >> message in error, please notify the sender immediately by e-mail >> and delete this email message from your computer. Thank you. > > > > 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 the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
