From simon.urbanek at r-project.org  Tue Jun 28 23:20:32 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 28 Jun 2011 17:20:32 -0400
Subject: [Rd] R CMD check --force-multiarch does not install all the
	archs for testing
In-Reply-To: <4E0A4381.6020506@fhcrc.org>
References: <4E0912EE.7020105@fhcrc.org>
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	<4E0A2507.1010904@fhcrc.org>
	<CA592CAB-B8DB-49C6-9AFD-9DB2C2087806@r-project.org>
	<4E0A2F44.3010109@fhcrc.org>
	<EBE00C6D-476A-4DA5-9CB8-A0F320D2B042@r-project.org>
	<4E0A4381.6020506@fhcrc.org>
Message-ID: <832A77AE-D195-413E-97D1-E26314F664E2@r-project.org>


On Jun 28, 2011, at 5:11 PM, Herv? Pag?s wrote:

> Simon,
> 
> On 11-06-28 01:44 PM, Simon Urbanek wrote:
>> 
>> On Jun 28, 2011, at 3:45 PM, Herv? Pag?s wrote:
>> 
>>> Hi Simon,
>>> 
>>> On 11-06-28 12:19 PM, Simon Urbanek wrote:
>>>> 
>>>> On Jun 28, 2011, at 3:01 PM, Herv? Pag?s wrote:
>>>> 
>>>>> Hi Uwe,
>>>>> 
>>>>> On 11-06-28 01:44 AM, Uwe Ligges wrote:
>>>>>> 
>>>>>> 
>>>>>> 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.
>>>>> 
>>>>> Why not just use this flag anyway? Does it hurt to use it on packages that don't strictly need it?
>>>>> 
>>>> 
>>>> It does for two reasons: a) everything is built twice
>>> 
>>> That's exactly what I want when I do 'R CMD check --force-multiarch'
>>> 
>> 
>> No, that's not what it does (and I assume you mean --force-biarch). It builds the package just once, you're simply overriding the default behavior of checking for configure.win, that's all. The two flags are orthogonal, --force-biarch makes no sense with --merge-multiarch, they are for all practical purposes mutually exclusive by definition of what they do.
> 
> I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check'
> has no --force-biarch option.
> 
>> 
>> 
>>>> and b) package authors don't expect the necessity to support --libs-only if the package doesn't require separate build runs.
>>> 
>>> When specifying --force-multiarch, the user really expects the package to be installed for all sub-archs.
>>> 
>> 
>> ... with the assumption that the package supports it even though it has a configure script which may to may not work unlike --merge-multiarch which will always work.
> 
> Just to clarify:
> 
> --force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL'
> option
> 
> --merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check'
> option
> 
> Now you are saying that --merge-multiarch will always work (on Windows
> of course, all this discussion is about how to achieve multiarch check
> on Windows). Great, this is what I've been observing too so far!
> On packages with or without native codes, with or without configure.win
> scripts, etc... It always seems to work. So, again, why isn't
> 'R CMD check --force-multiarch' installing with --merge-multiarch?
> Note that I'm not attached to that solution in particular, just trying
> to suggest an easy fix for 'R CMD check --force-multiarch' (which right
> now is broken on some packages).
> 
>> --force-biarch is just a way to flag packages that have configure.win that has no effect on the binary settings (flags etc.). It forces R to try multi-arch build in one flight, but it may or may not work depending on the package. It is a way to save time by not running --merge-multiarch (and thus building the package twice).
> 
> --force-biarch is an 'R CMD INSTALL' option that I don't use. Why would
> I use something that might fail when I can use --merge-multiarch which
> always works.
> 

Ok, never mind then, I was talking exclusively about R CMD INSTALL.

Cheers,
Simon


> Thanks,
> H.
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>>>> 
>>>> The cross-platform way is to not use --merge-multiarch but use --libs-only instead as needed (easy to check after the first arch run which will tell you whether it's needed or not). I suspect that --merge-multiarch is just a convenience shortcut (and it's unclear to me why it's Windows-only...).
>>> 
>>> A great convenience indeed as it allows to do the multiarch install in
>>> a single step. And it's unclear to me too why it's Windows-only but I
>>> would have hoped you would know...
>>> 
>>> Thanks,
>>> H.
>>> 
>>> 
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> 
>>>>>> 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.
>>>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> 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
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> 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
>>> 
>>> 
>> 
> 
> 
> -- 
> 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
> 
> 



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