Hi Malcolm, I am not sure why this is happening. I haven't been able to reproduce it on my system (which I think has a limit of 1024, so I had to increase your test case to exceed that). Does this happen when calling bgzip + indexTabix on a file 256 times? That would help to eliminate the complicated wrappers.
Thanks, Michael On Thu, Nov 8, 2012 at 2:32 PM, Cook, Malcolm <m...@stowers.org> wrote: > rtracklayer developers (Michael/Vincent/Robert), > > I find that tabix indexed exporting too many bed files causes an error. > > The session following my signature reproduces the error. > > It provides sessionInfo() details prior to the code causing the error > because sessionInfo() FAILS with 'too many open files' after running this > code (as does anything the opens files). > > The error does NOT occur when index=FALSE. Only when index=TRUE. > > I expect that the tabix calls are not cleaning up open file handles > correctly. > > uname -a tells me on my mac OSX that I can have 256 files open. > > The bug happens during the 253rd bedfile. > > openConnections() returns nothing. > > closeAllConnections() does not clean them up. > > lsof to list open files at the command line does NOT show them. > > Michael(?), you resolved a similar issue I once reported with rtracklayer > when creating bigBed files : > https://lists.soe.ucsc.edu/pipermail/genome/2012-February/028343.html > > Any suggestions for workarounds? Any possibility of a quick patch to > released rtracklayer? > > Thanks for rtracklayer! > > ~Malcolm Cook > ----------------------------------------------------------- > > bash-3.2$ R > > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(rtracklayer) > Loading required package: GenomicRanges > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames, > duplicated, eval, get, intersect, lapply, mapply, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff, > table, tapply, union, unique > > Loading required package: IRanges > Warning message: > package 'GenomicRanges' was built under R version 2.15.2 > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.18.0 GenomicRanges_1.10.4 IRanges_1.16.4 > BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] BSgenome_1.26.1 Biostrings_2.26.2 RCurl_1.95-3 > Rsamtools_1.10.1 XML_3.95-0.1 bitops_1.0-4.2 parallel_2.15.1 > stats4_2.15.1 tools_2.15.1 zlibbioc_1.4.0 > > > > x<-sapply(sprintf('deleteme_%s.bed',1:1000), function(conn) > {export(GRanges('X',IRanges(1,2)),conn,index=TRUE);1}) > Error in value[[3L]](cond) : index build failed > file: /Volumes/SAN1/Users/mec/deleteme/253.bed.gz > In addition: Warning message: > In doTryCatch(return(expr), name, parentenv, handler) : > [ti_index_build2] fail to create the index file. > > > > sessionInfo() > Error in gzfile(file, "rb") : cannot open the connection > In addition: Warning message: > In gzfile(file, "rb") : > cannot open compressed file > '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rtracklayer/Meta/package.rds', > probable reason 'Too many open files' > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
