Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing

From: Hervé Pagès <hpages_at_fhcrc.org>
Date: Tue, 28 Jun 2011 12:01:27 -0700

Hi Uwe,

On 11-06-28 01:44 AM, Uwe Ligges wrote:
>
>
> On 28.06.2011 01:31, Hervé Pagès wrote:
>> Hi,
>>
>> Why isn't 'R CMD check --force-multiarch' installing the package
>> for all the architectures that are going to be checked?

>
> Hervé,
>
> no, since it cannot know that that you need
>
> --merge-multiarch
>
> as an additional install flag for this particular package.

Why not just use this flag anyway? Does it hurt to use it on packages that don't strictly need it?

>
> 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

Whaoooo! Would be nice if there was a plan to make 'R CMD check' also usable by normal people (including the package developer), not just by a few privileged people that know about those undocumented tricks.

Thanks,
H.

>
> 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.
>>

-- 
Hervé Pagès

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

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