[BioC] Too many open files error with groupName = "all" in biocLite() call on Apple OS X

[Steven McKinney]

Apple MAC OS X 10.4
R version 2.3.1

Running biocLite() with groupName = "all"
does yield an OS error
"/Applications/R.app/Contents/Resources/sush: pipe error: Too many open files"

Is it possible to close files as the installation
proceeds?



> biocLite(groupName = "all", destdir = "/Volumes/KilroyHD/kilroy/Software/BioConductor")
Running getBioC version 0.1.6 with R version 2.3.1 
Running biocinstall version 1.8.4 with R version 2.3.1 
Your version of R requires version 1.8 of Bioconductor.
Will install the following packages:
            AnnBuilder                Biobase             Biostrings               Category       
...
...
...
   "widgetTools" 
                  xcms                y2hStat 
                "xcms"              "y2hStat" 
Please wait...

dependencies '‘EBImage’' are not availabledependencies '‘RMAGEML’' are not availabledependencies '‘RdbiPgSQL’' are not availabledependencies '‘genArise’' are not availabledependencies '‘iSPlot’' are not availabledependencies '‘maDB’' are not availabledependencies '‘pgUtils’' are not available

also installing the dependencies ‘coda’, ‘sp’, ‘XML’, ‘RSvgDevice’, ‘humanLLMappings’, ‘corpcor’, ‘longitudinal’, ‘locfdr’, ‘SSOAP’, ‘digest’, ‘MCMCpack’, ‘RCurl’, ‘e1071’, ‘randomForest’, ‘RGtk’, ‘gtkDevice’, ‘odesolve’, ‘YEAST’, ‘hgu95av2probe’, ‘combinat’, ‘pixmap’, ‘qtl’, ‘minpack.lm’, ‘ecoliLeucine’, ‘ecolicdf’, ‘LogicReg’, ‘ade4’, ‘cMAP’, ‘mda’, ‘splancs’, ‘fields’

trying URL 'http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.3/coda_0.10-5.tgz'
Content type 'application/x-gzip' length 169556 bytes
opened URL
==================================================
downloaded 165Kb

trying URL 'http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.3/sp_0.8-18.tgz'
Content type 'application/x-gzip' length 474078 bytes
opened URL
==================================================
downloaded 462Kb

trying URL 'http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.3/XML_0.99-8.tgz'
Content type 'application/x-gzip' length 745112 bytes
opened URL
==================================================
downloaded 727Kb
...
...
...

trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/powerpc/contrib/2.3/xcms_1.4.0.tgz'
Content type 'application/x-gzip' length 981589 bytes
opened URL
==================================================
downloaded 958Kb

trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/powerpc/contrib/2.3/y2hStat_1.2.0.tgz'
Content type 'application/x-gzip' length 7282072 bytes
opened URL
==================================================
downloaded 7111Kb

/Applications/R.app/Contents/Resources/sush: pipe error: Too many open files
/Applications/R.app/Contents/Resources/sush: pipe error: Too many open files
Error in sprintf(gettext(fmt, domain = domain), ...) : 
	argument is missing, with no default
In addition: Warning message:
number of rows of result
	is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 
> 






##############################################
(I can provide a full listing if needed for developers.)



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada