Hervé Pagès
2011-Jun-27 23:31 UTC
[Rd] R CMD check --force-multiarch does not install all the archs for testing
Hi,
Why isn't 'R CMD check --force-multiarch' installing the package
for all the architectures that are going to be checked?
For some packages, it only installs for the default arch ('i386').
Then testing the package for 'x64' fails.
For example,
Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz:
-----------------------------------------------------------
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-05-30 r56020)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies
... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the name space can be loaded with stated
dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ...Warning: running
command '"D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe"
R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save
--no-restore --slave -f
D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1
ERROR
Error: package 'fabia' is not installed for 'arch=x64'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
Content of fabia.Rcheck\00install.out:
--------------------------------------
* installing *source* package 'fabia' ...
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++ -c Rcpp.cpp -o Rcpp.o -I"D:/biocbld/BBS-2?1.9-B/R/include"
-I"D:/biocbld/BBS-2?1.9-B/R/src/include" -Wall -O2
ar r libRcpp.a Rcpp.o
C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a
ranlib libRcpp.a
rm -f Rcpp.o
rm -f Rcpp.o
** libs
running src/Makefile.win ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
g++ -c fabiac.cpp -o fabia.o -I../RcppSrc
-I"D:/biocbld/BBS-2?1.9-B/R/include" -Wall -O2
g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp
-L"D:/biocbld/BBS-2?1.9-B/R/bin/i386" -lR -o fabia.dll
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for "plot" from package
"graphics" in
package "fabia"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'fabia.Rnw'
** testing if installed package can be loaded
* DONE (fabia)
The source tarball for this package is available here:
http://bioconductor.org/packages/2.9/bioc/html/fabia.html
What command should be used to perform a multiarch check of this
package?
This is on a 64-bit Windows Server 2008 R2 Enterprise machine using a
recent combined Windows 32/64 bit binary of R-devel from CRAN.
Thanks!
H.
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Uwe Ligges
2011-Jun-28 08:44 UTC
[Rd] R CMD check --force-multiarch does not install all the archs for testing
On 28.06.2011 01:31, Herv? Pag?s wrote:> Hi, > > Why isn't 'R CMD check --force-multiarch' installing the package > for all the architectures that are going to be checked?Herv?, no, since it cannot know that that you need --merge-multiarch as an additional install flag for this particular package. You will have to check it in repository maintainer's mode (as the CRAN maintainers do everywhere). Essentially this is for me (when also producing WIndows binaries): Step 1: Installation R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch --library="D:/path/to/library" fabia_1.5.0.tar.gz > fabia-install.out 2>&1 (where the merge-multiarch part applies only to this package, of course) Step 2: Check (without installation, since that happened before already, using the install log from step 1) R CMD check --library="D:/path/to/library" --force-multiarch --install="check:fabia-install.out" fabia Best wishes, Uwe> For some packages, it only installs for the default arch ('i386'). > Then testing the package for 'x64' fails. > > For example, > > Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz: > ----------------------------------------------------------- > * using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck' > * using R version 2.14.0 Under development (unstable) (2011-05-30 r56020) > * using platform: i386-pc-mingw32 (32-bit) > * using session charset: ISO8859-1 > * using option '--no-vignettes' > * checking for file 'fabia/DESCRIPTION' ... OK > * this is package 'fabia' version '1.5.0' > * checking package name space information ... OK > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking whether package 'fabia' can be installed ... OK > * checking installed package size ... OK > * checking package directory ... OK > * checking for portable file names ... OK > * checking DESCRIPTION meta-information ... OK > * checking top-level files ... OK > * checking index information ... OK > * checking package subdirectories ... OK > * checking R files for non-ASCII characters ... OK > * checking R files for syntax errors ... OK > * loading checks for arch 'i386' > ** checking whether the package can be loaded ... OK > ** checking whether the package can be loaded with stated dependencies > ... OK > ** checking whether the package can be unloaded cleanly ... OK > ** checking whether the name space can be loaded with stated > dependencies ... OK > ** checking whether the name space can be unloaded cleanly ... OK > * loading checks for arch 'x64' > ** checking whether the package can be loaded ...Warning: running > command '"D:/biocbld/bbs-2.9-bioc/R/bin/x64/Rterm.exe" > R_ENVIRON_USER='no_such_file' --no-site-file --no-init-file --no-save > --no-restore --slave -f > D:\biocbld\bbs-2.9-bioc\tmpdir\RtmpO65p5H\Rin57456988' had status 1 > ERROR > Error: package 'fabia' is not installed for 'arch=x64' > Execution halted > > It looks like this package has a loading problem: see the messages for > details. > > Content of fabia.Rcheck\00install.out: > -------------------------------------- > > * installing *source* package 'fabia' ... > Building libRcpp.a in RcppSrc... > rm -f Rcpp.o libRcpp.a > g++ -c Rcpp.cpp -o Rcpp.o -I"D:/biocbld/BBS-2?1.9-B/R/include" > -I"D:/biocbld/BBS-2?1.9-B/R/src/include" -Wall -O2 > ar r libRcpp.a Rcpp.o > C:\Rtools213\MinGW\bin\ar.exe: creating libRcpp.a > ranlib libRcpp.a > rm -f Rcpp.o > rm -f Rcpp.o > ** libs > running src/Makefile.win ... > rm -f fabia.o fabia.dll *.a *.o *.so *.dll > g++ -c fabiac.cpp -o fabia.o -I../RcppSrc > -I"D:/biocbld/BBS-2?1.9-B/R/include" -Wall -O2 > g++ -shared -s -static-libgcc fabia.o -L../RcppSrc -lRcpp > -L"D:/biocbld/BBS-2?1.9-B/R/bin/i386" -lR -o fabia.dll > rm -f fabia.o *.a *.o *.so > installing to D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386 > ** R > ** demo > ** inst > ** preparing package for lazy loading > Creating a generic function for "plot" from package "graphics" in > package "fabia" > ** help > *** installing help indices > ** building package indices ... > *** tangling vignette sources ... > 'fabia.Rnw' > ** testing if installed package can be loaded > > * DONE (fabia) > > The source tarball for this package is available here: > http://bioconductor.org/packages/2.9/bioc/html/fabia.html > > What command should be used to perform a multiarch check of this > package? > > This is on a 64-bit Windows Server 2008 R2 Enterprise machine using a > recent combined Windows 32/64 bit binary of R-devel from CRAN. > > Thanks! > H. >