Hi there, By trying to do something that's not supposed to be done, I accidentally found a fatal R-killing issue with import.bw: I tried using import.bw on a bigWig file while it was still gzipped. You never know, sometimes these things work - I've since found an email thread that might help me avoid unpacking the file ( https://stat.ethz.ch/pipermail/bioconductor/2011-April/038734.html ) but in the meantime I thought I should tell you about how I made R die. Code to reproduce this, details and sessionInfo are all below. thanks, Janmet ######## library(rtracklayer) test.bw.file <- system.file("tests", "test.bw", package = "rtracklayer") ## import works, as it's supposed to bw <- import(test.bw.file, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7))) ### I copied that test.bw file to a local dir and used gzip to compress it test.bw.file.gz <- "temp/test.bw.gz" ### import gives error if I try to read in the gz file directly - that's OK bw2 <- import(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7))) ## Error in .importForFormat(format) : No import function for 'gz' found ## import.bw also works as its supposed to on the uncompressed file bw3 <- import.bw(test.bw.file, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7))) ## here's sessionInfo output, before I kill off R: sessionInfo() # R version 2.13.1 (2011-07-08) # Platform: i386-apple-darwin9.8.0/i386 (32-bit) # # locale: # [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 # # attached base packages: # [1] stats graphics grDevices utils datasets methods base # # other attached packages: # [1] rtracklayer_1.12.4 RCurl_1.6-7 bitops_1.0-4.1 # # loaded via a namespace (and not attached): # [1] Biostrings_2.20.2 BSgenome_1.20.0 GenomicRanges_1.4.6 IRanges_1.10.5 # [5] XML_3.4-2 ##### now, using import.bw on the gz file makes R crash with no error report on Mac bw4 <- import.bw(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7))) #### also see the same problem on linux, where my sessionInfo is as follows: # R version 2.13.1 (2011-07-08) # Platform: x86_64-unknown-linux-gnu (64-bit) # # locale: # [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C # [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 # [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 # [7] LC_PAPER=en_US.UTF-8 LC_NAME=C # [9] LC_ADDRESS=C LC_TELEPHONE=C # [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C # # attached base packages: # [1] stats graphics grDevices utils datasets methods base # # other attached packages: # [1] rtracklayer_1.12.4 RCurl_1.6-5 bitops_1.0-4.1 # # loaded via a namespace (and not attached): # [1] Biostrings_2.20.2 BSgenome_1.20.0 GenomicRanges_1.4.6 # [4] IRanges_1.10.5 XML_3.4-2

On Fri, Aug 12, 2011 at 1:53 PM, Janet Young <jayoung@fhcrc.org> wrote: > Hi there, > > By trying to do something that's not supposed to be done, I accidentally > found a fatal R-killing issue with import.bw: I tried using import.bw on a > bigWig file while it was still gzipped. > > Is there a reason to gzip a bigWig file? I think it already supports gzipped data blocks (but not a gzipped header, which is why this fails). See: http://comments.gmane.org/gmane.science.biology.ucscgenome.genera l/8900 > You never know, sometimes these things work - I've since found an email > thread that might help me avoid unpacking the file ( > https://stat.ethz.ch/pipermail/bioconductor/2011-April/038734.html ) but > in the meantime I thought I should tell you about how I made R die. > > Code to reproduce this, details and sessionInfo are all below. > > thanks, > > Janmet > > ######## > > library(rtracklayer) > > test.bw.file <- system.file("tests", "test.bw", package = "rtracklayer") > > ## import works, as it's supposed to > bw <- import(test.bw.file, ranges = GenomicRanges::GRanges("chr19", > IRanges(1, 6e7))) > > ### I copied that test.bw file to a local dir and used gzip to compress it > test.bw.file.gz <- "temp/test.bw.gz" > > ### import gives error if I try to read in the gz file directly - that's OK > bw2 <- import(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", > IRanges(1, 6e7))) > ## Error in .importForFormat(format) : No import function for 'gz' found > > I just added support for automatic decompression of gzip files, so this would no longer fail, in general. > > ## import.bw also works as its supposed to on the uncompressed file > bw3 <- import.bw(test.bw.file, ranges = GenomicRanges::GRanges("chr19", > IRanges(1, 6e7))) > > ## here's sessionInfo output, before I kill off R: > sessionInfo() > # R version 2.13.1 (2011-07-08) > # Platform: i386-apple-darwin9.8.0/i386 (32-bit) > # > # locale: > # [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > # > # attached base packages: > # [1] stats graphics grDevices utils datasets methods base > # > # other attached packages: > # [1] rtracklayer_1.12.4 RCurl_1.6-7 bitops_1.0-4.1 > # > # loaded via a namespace (and not attached): > # [1] Biostrings_2.20.2 BSgenome_1.20.0 GenomicRanges_1.4.6 > IRanges_1.10.5 > # [5] XML_3.4-2 > > > ##### now, using import.bw on the gz file makes R crash with no error > report on Mac > bw4 <- import.bw(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", > IRanges(1, 6e7))) > > > rtracklayer now catches exceptions thrown by Jim Kent's library, so R should no longer be aborted when things go wrong. In this case, since gzipped files are not supported, R will issue a warning and error to that effect. Thanks for this report, Michael > #### also see the same problem on linux, where my sessionInfo is as > follows: > # R version 2.13.1 (2011-07-08) > # Platform: x86_64-unknown-linux-gnu (64-bit) > # > # locale: > # [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > # [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > # [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > # [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > # [9] LC_ADDRESS=C LC_TELEPHONE=C > # [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > # > # attached base packages: > # [1] stats graphics grDevices utils datasets methods base > # > # other attached packages: > # [1] rtracklayer_1.12.4 RCurl_1.6-5 bitops_1.0-4.1 > # > # loaded via a namespace (and not attached): > # [1] Biostrings_2.20.2 BSgenome_1.20.0 GenomicRanges_1.4.6 > # [4] IRanges_1.10.5 XML_3.4-2 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]