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] on behalf of Dan
> Tenenbaum [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>
>> To: "bioc-devel" <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]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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