From hpages at fhcrc.org  Wed Sep 29 23:11:39 2010
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Wed, 29 Sep 2010 14:11:39 -0700
Subject: [Rd] More strange R CMD build/check errors on Windows
In-Reply-To: <4C8C6ECB.5080705@fhcrc.org>
References: <4C8C6ECB.5080705@fhcrc.org>
Message-ID: <4CA3AB8B.9020307@fhcrc.org>

Hi,

I can confirm that most of those "strange R CMD build/check errors"
we observe on Windows are actually a consequence of the "temp
Rscript file collision" I reported yesterday here:

   https://stat.ethz.ch/pipermail/r-devel/2010-September/058648.html

I just applied the following patch to the R we use for the Bioconductor
Windows builds:

Index: src/gnuwin32/system.c
===================================================================
--- src/gnuwin32/system.c	(revision 53067)
+++ src/gnuwin32/system.c	(working copy)
@@ -821,6 +821,8 @@

  #include <sys/stat.h>
  #include <time.h>
+#include <sys/types.h>
+#include <unistd.h>
  static int isDir(char *path)
  {
      struct stat sb;
@@ -1093,7 +1095,7 @@
  		}
  	    }
  	    srand( (unsigned) time(NULL) );
-	    sprintf(ifile, "%s/Rscript%x%x", tm, rand(), rand());
+	    sprintf(ifile, "%s/Rscript%dx%x", tm, getpid(), rand());
  	    ifp = fopen(ifile, "w+b");
  	    if(!ifp) R_Suicide(_("creation of tmpfile failed -- set TMPDIR 
suitably?"));
  	}

and the "strange R CMD build/check errors" are now all gone, except
those of the type:

   R\bin\R.exe CMD build baySeq
   * checking for file 'baySeq/DESCRIPTION' ... OK
   * preparing 'baySeq':
   * checking DESCRIPTION meta-information ... OK
   * installing the package to re-build vignettes
   * creating vignettes ...Warning in file(con, "r") :
     cannot open file 
'E:\biocbld\bbs-2.7-bioc\tmpdir\RtmpL9YTVu\xshell45ae180c': Permission 
denied
   Error in file(con, "r") : cannot open the connection
   Execution halted

I didn't initially report failures of this particular type because I
thought they might be yet another manifestation of the same bug but
apparently they are not (looks like it could be a temp file collision
again, but a different temp file now), so I'm going to report them in
a separate post.

Can the patch above be applied? Thanks!

H.


On 09/11/2010 11:10 PM, Herv? Pag?s wrote:
> Hi,
>
> This is a follow up to:
>
> https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html
>
> The Bioconductor daily builds have been reporting a lot of strange
> things lately on Windows using R-2.12. This started 2 or 3 months
> ago and things are not getting better with recent R-2.12.
> Here is a sample from today's build results. We use Windows Server
> 2003 R2 for the 32-bit builds, Windows Server 2008 R2 Enterprise
> for the 64-bit builds, and R-2.12 (2010-08-26 r52817) on both machines:
>
>
>  >>> On 64-bit Windows:
>
> R\bin\R.exe CMD build ACME
> --> produces no output at all and returns code 0.
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings affypdnn_1.23.0.tar.gz
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/affypdnn.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * using option '--no-vignettes'
> * checking for file 'affypdnn/DESCRIPTION' ... OK
> * this is package 'affypdnn' version '1.23.0'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'affypdnn' can be installed ...Warning in
> file(con, "r") :
> cannot open file
> 'E:/biocbld/bbs-2.7-bioc/meat/affypdnn.Rcheck/00install.out': No such
> file or directory
> Error in file(con, "r") : cannot open the connection
> Execution halted
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD build ArrayTools
> * checking for file 'ArrayTools/DESCRIPTION' ... OK
> * preparing 'ArrayTools':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to re-build vignettes
> -----------------------------------
> Warning: unknown option '-l'
> * checking for file
> 'E:\biocbld\bbs-2.7-bioc\tmpdir\Rtmpg0MxFa\Rinst69801ce4/DESCRIPTION'
> ... NO
> -----------------------------------
> ERROR: Installation failed
> Removing installation dir
>
>
>  >>> On 64-bit Windows:
>
> R\bin\R.exe CMD build baySeq
> * checking for file 'baySeq/DESCRIPTION' ... OK
> * preparing 'baySeq':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to re-build vignettes
> * creating vignettes ... ERROR
> Error: ERROR: no packages specified
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings BioSeqClass_1.7.0.tar.gz
> Warning: unknown option '--no-vignettes'
> Warning: unknown option '--timings'
> Converting Rd files to LaTeX ...
> BioSeqClass_1.7.0.tar.gz
> Warning in readLines(f) :
> incomplete final line found on 'BioSeqClass_1.7.0.tar.gz'
> Warning in parse_Rd("BioSeqClass_1.7.0.tar.gz", encoding = "unknown",
> fragment = FALSE, :
> BioSeqClass_1.7.0.tar.gz:2: unexpected UNKNOWN '\?'
> Warning: BioSeqClass_1.7.0.tar.gz:1: All text must be in a section
> Warning: BioSeqClass_1.7.0.tar.gz:2: All text must be in a section
> Warning: BioSeqClass_1.7.0.tar.gz:2: All text must be in a section
> Warning: BioSeqClass_1.7.0.tar.gz:3: All text must be in a section
> Warning: BioSeqClass_1.7.0.tar.gz:4: All text must be in a section
> Error : BioSeqClass_1.7.0.tar.gz: Sections \title, and \name must exist
> and be unique in Rd files
>
>
>  >>> On 64-bit Windows:
>
> R\bin\R.exe CMD build BufferedMatrix
> --> produces no output at all and returns code 0.
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings daMA_1.21.0.tar.gz
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/daMA.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * using option '--no-vignettes'
> * checking for file 'daMA/DESCRIPTION' ... OK
> * this is package 'daMA' version '1.21.0'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'daMA' can be installed ...Warning in
> file(con, "r") :
> cannot open file
> 'E:/biocbld/bbs-2.7-bioc/meat/daMA.Rcheck/00install.out': No such file
> or directory
> Error in file(con, "r") : cannot open the connection
> Execution halted
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings ddCt_1.3.2.tar.gz
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/ddCt.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * using option '--no-vignettes'
> * checking for file 'ddCt/DESCRIPTION' ... OK
> * this is package 'ddCt' version '1.3.2'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'ddCt' can be installed ...Warning in
> file(con, "r") :
> cannot open file
> 'E:/biocbld/bbs-2.7-bioc/meat/ddCt.Rcheck/00install.out': No such file
> or directory
> Error in file(con, "r") : cannot open the connection
> Execution halted
>
>
>  >>> On 64-bit Windows:
>
> R\bin\R.exe CMD build GEOmetadb
> * checking for file 'GEOmetadb/DESCRIPTION' ... OK
> * preparing 'GEOmetadb':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to re-build vignettes
> * creating vignettes ... ERROR
> Error: ERROR: no packages specified
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings IRanges_1.7.33.tar.gz
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/IRanges.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * using option '--no-vignettes'
> * checking for file 'IRanges/DESCRIPTION' ... OK
> * this is package 'IRanges' version '1.7.33'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'IRanges' can be installed ... ERROR
> Installation failed.
> See 'E:/biocbld/bbs-2.7-bioc/meat/IRanges.Rcheck/00install.out' for
> details.
>
> Content of IRanges.Rcheck/00install.out:
>
> * install options '--no-html --no-multiarch'
>
> Warning: unknown option '-l'
> Warning: unknown option '--no-html'
> Warning: unknown option '--no-multiarch'
> Error in .pkg2tex(files, outfile, encoding = encoding, append = append, :
> this package does not have either a 'latex' or a (source) 'man' directory
>
>
>  >>> On 32-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings keggorthology_2.1.1.tar.gz
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/keggorthology.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * using option '--no-vignettes'
> * checking for file 'keggorthology/DESCRIPTION' ... OK
> * this is package 'keggorthology' version '2.1.1'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'keggorthology' can be installed ... ERROR
> Installation failed.
> See 'E:/biocbld/bbs-2.7-bioc/meat/keggorthology.Rcheck/00install.out'
> for details.
>
> Content of keggorthology.Rcheck/00install.out:
>
> * install options '--no-html --no-multiarch'
>
> Warning: unknown option '--no-html'
> * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/KEGGOR?1.Rcheck'
> * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817)
> * using platform: i386-pc-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * checking for file 'KEGGOR?1/DESCRIPTION' ... OK
> * this is package 'keggorthology' version '2.1.1'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'keggorthology' can be installed ... 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
> * checking whether the package can be loaded ... ERROR
> Error in library(KEGGOR ? 1) : 'package' must be of length 1
> Execution halted
>
> It looks like this package has a loading problem: see the messages for
> details.
>
>
>  >>> On 64-bit Windows:
>
> R\bin\R.exe CMD check --no-vignettes --timings OLIN_1.27.0.tar.gz
> Warning: unknown option '--no-vignettes'
> Warning: unknown option '--timings'
> Converting Rd files to LaTeX ...
> OLIN_1.27.0.tar.gz
> Warning in readLines(f) :
> incomplete final line found on 'OLIN_1.27.0.tar.gz'
> Warning in parse_Rd("OLIN_1.27.0.tar.gz", encoding = "unknown", fragment
> = FALSE, :
> OLIN_1.27.0.tar.gz:2: unexpected '}'
> Warning in parse_Rd("OLIN_1.27.0.tar.gz", encoding = "unknown", fragment
> = FALSE, :
> OLIN_1.27.0.tar.gz:4: unexpected '}'
> Warning in parse_Rd("OLIN_1.27.0.tar.gz", encoding = "unknown", fragment
> = FALSE, :
> OLIN_1.27.0.tar.gz:7: unexpected '{'
> Warning in parse_Rd("OLIN_1.27.0.tar.gz", encoding = "unknown", fragment
> = FALSE, :
> OLIN_1.27.0.tar.gz:8: unexpected '}'
> Warning: OLIN_1.27.0.tar.gz:1: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:2: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:2: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:2: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:2: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:3: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:4: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:4: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:4: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:5: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:6: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:7: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:7: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:7: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:8: All text must be in a section
> Warning: OLIN_1.27.0.tar.gz:8: All text must be in a section
> Error : OLIN_1.27.0.tar.gz: Sections \title, and \name must exist and be
> unique in Rd files
>
>
>  >>> and so on...
>
>
> AFAICT those problems were never seen before (i.e. with R < 2.12).
> They show up randomly everyday for a small number of packages
> (between 10 and 20 out of 400). The set of victims changes everyday
> and any package seems to be a potential victim (I've not been able
> to observe any obvious pattern so far).
> Does anyone have any idea what could make 'R CMD build' and
> 'R CMD check' so confused/unreliable on Windows?
>
> 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] More strange R CMD build/check errors on Windows
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