Question: segfault with rmaMicroRna in AgiMicroRna package
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gravatar for heyi xiao
9.6 years ago by
heyi xiao360
United States
heyi xiao360 wrote:
Dear Pedro, I am using AgiMicroRna 1.0.0 to process my agilent miRNA microarray data. Agilent Feature Extraction Software v10.7 was used to extract the features. I got segfault when I do rmaMicroRna:  > dd.rma=rmaMicroRna(dd.micro, +  normalize=TRUE, +  background=TRUE)   *** caught segfault *** address 0x10cd6000, cause 'memory not mapped'  However, this problem is gone when I do rmaMicroRna on a subset of my dd.micro: > dd.rma=rmaMicroRna(dd.micro[,13:16], +  normalize=TRUE, +  background=TRUE)  I have check my dd.micro data, everything is fine. In other words, rmaMicroRna only works when I apply it to a smaller dataset. BTW, I am using a 64 bit version of R on linux machine. Therefore, memory limit shouldn’t be an issue here. Could you look at this issue? Thanks a lot! Heyi  PS: my session information: > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu  locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C  attached base packages: [1] stats     graphics grDevices utils     datasets  methods  base     other attached packages: [1] AgiMicroRna_1.0.0   preprocessCore_1.6.0 affy_1.22.0        [4] limma_2.18.0        Biobase_2.4.1       loaded via a namespace (and not attached): [1] affyio_1.12.0 [[alternative HTML version deleted]]
process agimicrorna • 559 views
ADD COMMENTlink modified 9.6 years ago by Seth Falcon7.4k • written 9.6 years ago by heyi xiao360
Answer: segfault with rmaMicroRna in AgiMicroRna package
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gravatar for Seth Falcon
9.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Heyi, A couple of suggestions to help you get help more quickly. 1. Try upgrading your R and Bioconductor packages to the latest release and see if that resolves the problem for you. 2. If you still see the crash, since you are running on Linux you should be able to extract some further debugging information that will be useful to the package maintainer. Do as follows: bash$ R -d gdb (gdb) run R> # run your example to get the crash (gdb) bt 15 Send the output of the backtrace to help identify where things are going astray. + seth On 4/30/10 3:48 PM, heyi xiao wrote: > > > > > Dear Pedro, > > I am using AgiMicroRna 1.0.0 to process my agilent miRNA > microarray data. Agilent Feature Extraction Software v10.7 was > used to extract the features. I got segfault when I do rmaMicroRna: > > > >> dd.rma=rmaMicroRna(dd.micro, > > + normalize=TRUE, > > + background=TRUE) > > > > *** caught segfault *** > > address 0x10cd6000, > cause 'memory not mapped' > > > > However, this > problem is gone when I do rmaMicroRna on a subset of my dd.micro: > >> dd.rma=rmaMicroRna(dd.micro[,13:16], > > + normalize=TRUE, > > + background=TRUE) > > > > I have check my dd.micro > data, everything is fine. In other words, rmaMicroRna only works when I apply > it to a smaller dataset. BTW, I am using a 64 bit version of R on linux > machine. Therefore, memory limit shouldn?t be an issue here. Could you look at > this issue? Thanks a lot! > > Heyi > > > > PS: my session information: > >> sessionInfo() > > R version 2.9.0 > (2009-04-17) > > x86_64-unknown-linux-gnu > > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > > > attached base > packages: > > [1] stats graphics > grDevices utils datasets methods > base > > > > other attached > packages: > > [1] AgiMicroRna_1.0.0 > preprocessCore_1.6.0 affy_1.22.0 > > > [4] limma_2.18.0 > Biobase_2.4.1 > > > > loaded via a > namespace (and not attached): > > [1] affyio_1.12.0 > > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Seth Falcon Bioconductor Core Team | FHCRC
ADD COMMENTlink written 9.6 years ago by Seth Falcon7.4k
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