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

[Brad Friedman]

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. 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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