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R CMD check --force-multiarch does not install all the archs for testing

9 messages · Uwe Ligges, Simon Urbanek, Hervé Pagès

Original
Hervé Pagès
# 
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.
Uwe Ligges
#
On 28.06.2011 01:31, Herv? Pag?s wrote:
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
Hervé Pagès
# 
Hi Uwe,
On 11-06-28 01:44 AM, Uwe Ligges wrote:
Why not just use this flag anyway? Does it hurt to use it on packages
that don't strictly need it?
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.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Jun 28, 2011, at 3:01 PM, Herv? Pag?s wrote:

        

            

      
      
      
    

        
It does for two reasons: a) everything is built twice and b) package authors don't expect the necessity to support --libs-only if the package doesn't require separate build runs.

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...).

Cheers,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi Simon,

        
On 11-06-28 12:19 PM, Simon Urbanek wrote:

            

      
      
      
    

        
That's exactly what I want when I do 'R CMD check --force-multiarch'

            

      
      
      
    

        
When specifying --force-multiarch, the user really expects the package
to be installed for all sub-archs.

            

      
      
      
    

        
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.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Jun 28, 2011, at 3:45 PM, Herv? Pag?s wrote:

        

            

      
      
      
    

        
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.

            

      
      
      
    

        
... 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. --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).

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Simon,

        
On 11-06-28 01:44 PM, Simon Urbanek wrote:

            

      
      
      
    

        
I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check'
has no --force-biarch option.

            

      
      
      
    

        
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 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.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

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

        

            

      
      
      
    

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

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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On 28.06.2011 23:11, Herv? Pag?s wrote:

            

      
      
      
    

        
It does not "always work", unfortunately. We need force-biarch on CRAN for:

RGtk2
rgdal
rphast
SQLiteMap

            

      
      
      
    

        
Well, merge-multiarch will result in small overhead. It will try to 
compile the code in ./src  for the other architecture and merge that 
into the same package. For packages without any compiled code, it does 
not make sense to ask R to do that since the packages are identical 
under 32-bit and 64-bit, hence you don't want the overhead. For packages 
that include compiled code, you still do not want it, since R does it 
automatically - unless there is a configure.win file.

Therefore, the option is just an add on that is necessary for only 18 
out of roughly 3000 CRAN packages.

So we have 4 packages that require --force-biarch and 18 requiring 
--merge-multiarch on CRAN. All the others build automatically for both 
architectures if they need to. So no reason to do that all the time.

Best wishes,
Uwe

            

      
      
      
    

        
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