[BioC] cause 'memory not mapped' when use oligo
Jianhong.Ou at umassmed.edu
Wed Sep 26 22:10:57 CEST 2012
I followed your code and installed affxparser from aroma. And it works!!!
Thanks a lot for that.
jianhong.ou at umassmed.edu
On Sep 26, 2012, at 3:50 PM, Henrik Bengtsson wrote:
> I'm rather sure this is related to the 'affxparser' package. More
> specifically, this problem occurs only for OSX users who have
> installed the OSX binary distribution of affxparser available from
> Bioconductor. As far as I understand it, it appears to be a
> Bioconductor server farm configuration. BioC (Dan Tenenbaum) has
> helped us (maintainers of affxparser) trying to figure out what's
> causing this, but still to date it remains a "mystery" why the BioC
> OSX binaries for affxparser causes core dumps. It appears to only
> happen on the BioC farm. As a workaround, we've built a separate OSX
> binary for affxparser that can be installed via:
> That script will check your current setup decide whether the
> workaround or the default BioC built will be installed, i.e. anyone
> who wish to install affxparser can use that script. The script will
> also run validation tests to assert that the installed version of
> affxparser works properly. (Those tests are only available for
> affxparser >= 1.29.2 (BioC devel)). The tests can be ran separately
> too by
> Jianhong, please report back and let us know if this solved your
> original problem.
> On Tue, Sep 25, 2012 at 3:51 PM, Benilton Carvalho
> <Benilton.Carvalho at cancer.org.uk> wrote:
>> Most likely a damaged file. Check all the file sizes (I'd go to the terminal and run "du -hsc *.CEL" (without quotes). My guess is that most of them will be about the size size and one will show a strange (usual smaller) value, and this one is a strong candidate for being the problematic file.
>> Sent from a mobile device. Please apologise for brevity, spelling and punctuation.
>> Robert Scharpf <rscharpf at jhsph.edu> wrote:
>> This could be a corrupt file. try reading the cel headers directly:
>> for(i in seq_along(celfiles)) readCelHeader(celfiles[i])
>> On Sep 25, 2012, at 4:21 PM, "Ou, Jianhong" <Jianhong.Ou at umassmed.edu> wrote:
>>> Hi all,
>>> When I run oligo to analysis the data of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7822 at Mac OS X (10.6.8), the R always crash. How could I figure out this? Here is my codes and sessionInfo.
>>> Loading required package: oligoClasses
>>> Loading package bit 1.1-8
>>> package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
>>> creators: bit bitwhich
>>> coercion: as.logical as.integer as.bit as.bitwhich which
>>> operator: ! & | xor != ==
>>> querying: print length any all min max range sum summary
>>> bit access: length<- [ [<- [[ [[<-
>>> for more help type ?bit
>>> Loading package ff2.2-7
>>> - getOption("fftempdir")=="/var/folders/Dj/Dj+bWjS7HxiNJ0kYFeKdTE+++TI/-Tmp-//RtmpPa6Fh5"
>>> - getOption("ffextension")=="ff"
>>> - getOption("ffdrop")==TRUE
>>> - getOption("fffinonexit")==TRUE
>>> - getOption("ffpagesize")==65536
>>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
>>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
>>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
>>> Welcome to oligoClasses version 1.18.0
>>> Welcome to oligo version 1.20.4
>>>> celfiles <- c(paste("GSM1879", 38:49, ".CEL", sep=""), paste("GSM1881", 16:22, ".CEL", sep=""))
>>> Loading required package: RSQLite
>>> Loading required package: DBI
>>>> crlmm(celfiles, "hindIIout")
>>> *** caught segfault ***
>>> address 0xfffffffc, cause 'memory not mapped'
>>> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
>>> 2: readCelHeader(filenames)
>>> 3: tolower(x)
>>> 4: paste("pd.", tolower(x), sep = "")
>>> 5: gsub("[_-]", ".", paste("pd.", tolower(x), sep = ""))
>>> 6: cleanPlatformName(readCelHeader(filenames)$chiptype)
>>> 7: crlmm(celfiles, "hindIIout")
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>> R version 2.15.1 (2012-06-22)
>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>>  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> attached base packages:
>>>  stats graphics grDevices utils datasets methods base
>>> other attached packages:
>>>  pd.mapping50k.hind240_1.6.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.20.4 oligoClasses_1.18.0
>>> loaded via a namespace (and not attached):
>>>  affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.25.8 bit_1.1-8
>>>  codetools_0.2-8 ff_2.2-7 foreach_1.4.0 IRanges_1.15.24 iterators_1.0.6 preprocessCore_1.18.0 splines_2.15.1
>>>  stats4_2.15.1 zlibbioc_1.2.0
>>> Yours sincerely,
>>> Jianhong Ou
>>> jianhong.ou at umassmed.edu<mailto:jianhong.ou at umassmed.edu>
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