Question: Too many open files error with groupName = "all" in biocLite() call on Apple OS X
0
gravatar for Steven McKinney
13.3 years ago by
Steven McKinney310 wrote:
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/power pc/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/power pc/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
ADD COMMENTlink modified 13.3 years ago by Seth Falcon7.4k • written 13.3 years ago by Steven McKinney310
Answer: Too many open files error with groupName = "all" in biocLite() call on Apple OS
0
gravatar for Seth Falcon
13.3 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi Steven, "Steven McKinney" <smckinney at="" bccrc.ca=""> writes: > 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? You would think so :-) Would you be willing to send this report to the R-sig-mac list? I'm pretty sure the issues you've encountered are R/Mac specific and not BioC specific. Herve posted there a note regarding the cbind warning you reported and I think I have a fix for it. + seth
ADD COMMENTlink written 13.3 years ago by Seth Falcon7.4k
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