From hpages at fhcrc.org  Tue Jun 28 23:11:29 2011
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Tue, 28 Jun 2011 14:11:29 -0700
Subject: [Rd] R CMD check --force-multiarch does not install all the
 archs for testing
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	<4E099478.4030609@statistik.tu-dortmund.de>
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	<4E0A2F44.3010109@fhcrc.org>
	<EBE00C6D-476A-4DA5-9CB8-A0F320D2B042@r-project.org>
Message-ID: <4E0A4381.6020506@fhcrc.org>

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.

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
=?windows-1252?Q?Herv=E9_Pag=E8s?=