[BioC] cause 'memory not mapped' when use oligo
Ou, Jianhong
Jianhong.Ou at umassmed.edu
Wed Sep 26 22:10:57 CEST 2012
Dear Henrik,
I followed your code and installed affxparser from aroma. And it works!!!
Thanks a lot for that.
Yours sincerely,
Jianhong Ou
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:
>
> 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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> NOTICE AND DISCLAIMER
>> This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose.
>>
>> We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you.
>> Cancer Research UK
>> Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103)
>> A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F).
>> Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list