From hpages at fhcrc.org  Thu Jun 10 23:16:04 2010
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Thu, 10 Jun 2010 14:16:04 -0700
Subject: [Rd] R-based version of R CMD build broken on Windows
Message-ID: <4C115614.9080803@fhcrc.org>

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?

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
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