[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

[Dan Tenenbaum]

----- Original Message -----
> From: "Brad Friedman" <friedman.brad at gene.com>
> To: "bioc-devel" <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
> 
> 
> 
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