On 03/21/2011 07:22 PM, Simon Urbanek wrote:
On Mar 21, 2011, at 9:07 PM, Dan Tenenbaum wrote:
Hello,
I have come across two separate packages that have a Makefile in inst/doc
which use the R_HOME variable.
In both cases, the path to R_HOME gets munged in such a way that commands
that include R_HOME fail on Windows:
For example, one Makefile, for the xmapcore package (
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password:
readonly) has this:
R=${R_HOME}/bin/R
SUITE=../cookbook/delia.R
[...]
${R} --vanilla --verbose< ${SUITE}
the output of trying to build this package includes:
* creating vignettes ... ERROR
E:\biocbld\BBS-2~1.8-B\R/bin/R --vanilla --verbose< ../cookbook/delia.R
E:biocbldBBS-2~1.8-BR/bin/R: not found
make: *** [pdf] Error 127
Error in tools::buildVignettes(dir = ".") : running 'make' failed
Execution halted
It seems R_HOME is not getting resolved to a valid path. That's strange
because R CMD echo shows the right thing:
E:\sandbox>\biocbld\bbs-2.8-bioc\R\bin\R CMD echo %R_HOME%
e:/biocbld/bbs-2.8-bioc/R
That's a nice path with all forward slashes and no funny 8.3 paths with
tildes. But it looks like when R_HOME is invoked in a Makefile, the
resulting path has a mix of forward and backslashes,
Nope, at least not in R from CRAN:
Makevars:
all:
echo R_HOME: $(R_HOME)
[...]
echo R_HOME: c:/PROGRA~1/R/R-212~1.2
R_HOME: c:/PROGRA~1/R/R-212~1.2
But I see that you have custom rhome setting (BBS...) so changes are that is
the culprit - the rhome for that R build is set incorrectly to contain
backslashes.
Not sure about the Makefile, but see
https://stat.ethz.ch/pipermail/r-devel/2011-March/060260.html
also on my own machine
Z:\> R CMD INSTALL Biobase
* installing to library 'C:\Users\User\Documents/R/win-library/2.13'
* installing *source* package 'Biobase' ...
...
** testing if installed package can be loaded
Error: '\U' used without hex digits in character string starting "C:\U"
Execution halted
ERROR: loading failed
* removing 'C:\Users\User\Documents/R/win-library/2.13/Biobase'
* restoring previous 'C:\Users\User\Documents/R/win-library/2.13/Rsamtools'
whereas under 2.12
Z:\>R CMD INSTALL Biobase
* installing to library 'C:\Users\User\Documents/R/win-library/2.12'
* installing *source* package 'Biobase' ...
and everything is fine.
Z:\> R --version
R version 2.13.0 alpha (2011-03-17 r54849)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Cheers,
Simon
and gets translated
into 8.3 style, and the resulting path is not valid for finding R
executables.
Note that R_HOME is defined within R; I don't also have it defined at the
shell level:
E:\sandbox>echo %R_HOME%
%R_HOME%
Any ideas?
Thanks,
Dan
sessionInfo()
R version 2.13.0 alpha (2011-03-18 r54865)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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