From hpages at fhcrc.org  Fri Jun 11 19:20:21 2010
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Fri, 11 Jun 2010 10:20:21 -0700
Subject: [Rd] R-based version of R CMD build broken on Windows
In-Reply-To: <4C11F869.1070806@statistik.tu-dortmund.de>
References: <4C115614.9080803@fhcrc.org>
	<4C11F869.1070806@statistik.tu-dortmund.de>
Message-ID: <4C127055.6040108@fhcrc.org>



Uwe Ligges wrote:
> 
> 
> On 10.06.2010 23:16, Herv? Pag?s wrote:
>> Hi,
>>
>> The R-based version of R CMD build doesn't work for me on Windows:
>>
>> E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase
>> * checking for file 'meat\Biobase/DESCRIPTION' ... OK
>> * preparing 'Biobase':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to re-build vignettes
>> Warning in shell(sprintf("%s > %s 2>&1", command, outfile), shell =
>> "cmd.exe") :
>> '"E:\biocbld\bbs-2.7-bioc\R/bin/i386/Rcmd.exe" INSTALL -l
>> "C:\DOCUME~1\BIOCBU~1\LOCALS~1\tmpdir\RtmpfEAMUM\Rinst4488262f"
>> "E:/biocbld/bbs-2.7-bioc/meat/Biobase" >
>> C:\DOCUME~1\BIOCBU~1\LOCALS~1\tmpdir\RtmpfEAMUM\xshell2bc3cf 2>&1'
>> execution failed with error code 1
>> -----------------------------------
>> The filename, directory name, or volume label syntax is incorrect.
>> -----------------------------------
>> ERROR: Installation failed
>> Removing installation dir
>>
>> The old Perl-based version (R\bin\R CMD obuild) does work with no 
>> problem.
>>
>> My R version is:
>>
>> E:\biocbld\bbs-2.7-bioc>R\bin\R --version
>> R version 2.12.0 Under development (unstable) (2010-06-07 r52225)
>> Copyright (C) 2010 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under the terms of the
>> GNU General Public License version 2.
>> For more information about these matters see
>> http://www.gnu.org/licenses/.
>>
>> I'm on Windows Server 2003 R2 (32-bit). I have the same problem on
>> Windows Server 2008 R2 Enterprise (64-bit) (using the same revision
>> of R 2.12.0). I don't have any problem on Linux or Mac OS X.
>>
>> FYI, this problem is causing most of the Bioconductor packages to
>> be red on Windows on our daily build/check report:
>>
>> http://bioconductor.org/checkResults/2.7/bioc-LATEST/
>>
>> OTOH I don't see anything like that on the check summaries for
>> CRAN packages:
>>
>> http://cran.r-project.org/web/checks/check_summary.html
>>
>> Maybe because CRAN only runs R CMD check which is still Perl-based?
> 
> 
> No, but because the Windows checks on that page are not yet available 
> for R-devel.

Ah right (oops).  Thx,

H.

> 
> Best,
> Uwe Ligges
> 
> 
>> Thanks,
>> H.
>>

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] R-based version of R CMD build broken on Windows
=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=