[BioC] cause 'memory not mapped' when use oligo

Henrik Bengtsson hb at biostat.ucsf.edu
Wed Sep 26 21:50:10 CEST 2012


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:

source("http://aroma-project.org/affxparser.R");
installAffxparser();

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

source("http://aroma-project.org/affxparser.R");
testAffxparser();

Jianhong, please report back and let us know if this solved your
original problem.

/Henrik
(affxparser)




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:
> Jianhong,
>
> This could be a corrupt file.  try reading the cel headers directly:
>
> library(affxparser)
> file.exists(celfiles)
> for(i in seq_along(celfiles)) readCelHeader(celfiles[i])
>
> Rob
>
>
> 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.
>>
>>> library(oligo)
>> 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=""))
>>> library("pd.mapping50k.hind240")
>> Loading required package: RSQLite
>> Loading required package: DBI
>>> crlmm(celfiles, "hindIIout")
>>
>> *** caught segfault ***
>> address 0xfffffffc, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
>> 2: readCelHeader(filenames[1])
>> 3: tolower(x)
>> 4: paste("pd.", tolower(x), sep = "")
>> 5: gsub("[_-]", ".", paste("pd.", tolower(x), sep = ""))
>> 6: cleanPlatformName(readCelHeader(filenames[1])$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
>>
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] 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):
>> [1] 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
>> [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
>> [15] stats4_2.15.1         zlibbioc_1.2.0
>>
>>
>> Yours sincerely,
>>
>> Jianhong Ou
>>
>> jianhong.ou at umassmed.edu<mailto:jianhong.ou at umassmed.edu>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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