Re: [Rd] R-based version of R CMD build broken on Windows
On 10.06.2010 23:16, Hervé Pagès 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.
Best,
Uwe Ligges
Thanks,
H.
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[Rd] CHM help does not find help docs in package stats
Hi all, currently I'm working on an R package bundling some frequently used functions. When I load my package and type ?one_of_my_functions I get the particular help file. If I try to get help on another function, which is part of package stats (prcomp say), I get "This program cannot display the webpage". A help on ?mean does, however, work as it opens a new window showing the help on mean. There is another peculiarity, if it happens that I requested a help file for a function in the package stats before I used the help on one of my functions, everything works out fine. Does anybody know how I can get rid of this annoying behavior? It has to have something to do with my particular package, since everything works as expected with another package of mine. I override one of the functions of stats (biplot.default), which is, however, not exported and resides within my namespace. Could that be the reason? Any help highly appreciated. Thanks + BR, Thorn __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] OWL ontologies in R?
The Rredland package available through Bioconductor (www.bioconductor.org) will parse and do limited modeling of RDF; some OWL examples are in the vignette. Some years ago a package called Rswub included an interface to Jena, but became stale. Developments in R-java interfaces since then might make an effect R-Jena interface relatively easy to create and maintain. It has been noted that Rredland's dependence on Berkeley db is a potential nuisance for installation; since Rredland was released, a SQLite back end has been introduced for redland/librdf but I have not had the opportunity to add code to capitalize on this. Patches welcome. On Thu, Jun 10, 2010 at 3:45 PM, Stavros Macrakis wrote: > Are there any R packages to import and use Web Ontology Language (OWL) > ontologies (represented in OWL/RDF or other form)? > > Thanks, > > -s > >[[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-based version of R CMD build broken on Windows
Uwe Ligges wrote:
On 10.06.2010 23:16, Hervé Pagès 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.
--
Hervé Pagès
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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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[Rd] support for radix order() over entire range of integers
Hi, Is there any good reason not to allow radix sorting via order() over the entire range of R (32bit) integers, instead of setting a hard limit at 100,000? Many machines have plenty of memory to support this. Seems like it is just a matter of dynamic allocating the bucket array instead of the current static allocation. This would really help with e.g. sorting positions in the genome. I'm happy to submit a patch if this sounds sensible. Thanks, Michael [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
