[BioC] Rsubread crashes in 32bit linux
Wei Shi
shi at wehi.EDU.AU
Wed Jun 6 12:56:00 CEST 2012
Dear Peter,
It looks like your installation of Rsubread was unsuccessfully, therefore
you got an error when you loaded it into your R session. This issue is
different from the issue with running buildindex() function on a 32-bit
machine.
Did you notice any errors when it was being installed? You can reinstall
it using the following commands in your R session:
source("http://bioconductor.org/biocLite.R")
biocLite("Rsubread")
Cheers,
Wei
> Dear Wei,
> I also encounter a (perhaps related) problem using Rsubread (see below).
> Kind regards
> Peter
>
>
>> library(Rsubread)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/opt/ghpc/R-2.15.0/lib64/R/library/Rsubread/libs/Rsubread.so':
> /opt/ghpc/R-2.15.0/lib64/R/library/Rsubread/libs/Rsubread.so: cannot map
> zero-fill pages: Cannot allocate memory
> Error: package/namespace load failed for 'Rsubread'
>> ref <- system.file("extdata","reference.fa",package="Rsubread")
>> path <- system.file("extdata",package="Rsubread")
>> buildindex(basename=file.path(path,"reference_index"),reference=ref)
> Error: could not find function "buildindex"
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>>
>
>
> ________________________________________
> From: bioconductor-bounces at r-project.org
> [bioconductor-bounces at r-project.org] On Behalf Of Dan Du
> [tooyoung at gmail.com]
> Sent: Wednesday, June 06, 2012 8:50 AM
> To: Wei Shi
> Cc: Yang Liao; bioconductor at r-project.org mailman
> Subject: Re: [BioC] Rsubread crashes in 32bit linux
>
> Dear Wei,
>
> Unfortunately reducing the memory parameter to 1000, still causes the
> segfault. I guess with 3g ram limit on a 32bit system, there is still a
> fat chance that you can not request a continuous 1g block.
>
> For that 64bit laptop, it is still strange about the 6g memory draining.
> It is happing during the installation when compiling the shared library
> Rsubread.so, not running the buildindex function. Btw, the gcc version
> is 4.4.3.
>
> Server and opensuse box runs gcc version 4.3.1 and 4.5.0 respectively.
>
> Regards,
> Dan
>
> On Wed, 2012-06-06 at 14:56 +1000, Wei Shi wrote:
>> Dear Dan,
>>
>> It is probably because including genome sequences into the index slowed
>> down your laptop. But I believe it should be alleviated if you give
>> smaller values to the 'memory ' parameter of the buildindex() function.
>> Also, the index building is an one-off operation, you do not need to
>> redo it even when new releases come.
>>
>> For your 32-bit opensuse box, I guess the problem will be solved if you
>> change the amount of memory requested to be 1000MB.
>>
>> Cheers,
>> Wei
>>
>> On Jun 5, 2012, at 11:43 PM, Dan Du wrote:
>>
>> > Hi Robert,
>> >
>> > I have been experiencing something else, possibly related to yours,
>> > on a 64bit ubuntu laptop with 6g of ram.
>> >
>> > As I recall, when bumping to Bioc 2.10, the Rsubread installation kind
>> > of ate all the memory, basically froze the system so I had to call it
>> > off, yet building it on the server side turned out fine. So I think I
>> > just accepted that the new version may be 'computationally heavy' thus
>> > not suitable for a normal pc, though I did not find any mentioning of
>> > this increased memory requirement in the NEWS file.
>> >
>> > So currently Rsubread stays at 1.4.4 on that pc, all subsequent
>> versions
>> > of Rsubread drain the memory in the same way when compiling
>> Rsubread.so.
>> >
>> > Now I think I can confirm this on a 32-bit opensuse box, it did
>> > successfully built, but when running the example code in the manual,
>> > same segfault happens.
>> >
>> >
>> >> library(Rsubread)
>> >> ref <- system.file("extdata","reference.fa",package="Rsubread")
>> >> path <- system.file("extdata",package="Rsubread")
>> >> buildindex(basename=file.path(path,"reference_index"),reference=ref)
>> >
>> > Building a base-space index.
>> > Size of memory used=3700 MB
>> > Base name of the built index
>> > = /home/opensuse/R-patched/library/Rsubread/extdata/reference_index
>> >
>> > *** caught segfault ***
>> > address 0xdf03ee80, cause 'memory not mapped'
>> >
>> > Traceback:
>> > 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv =
>> > as.character(cmd), PACKAGE = "Rsubread")
>> > 2: buildindex(basename = file.path(path, "reference_index"), reference
>> > = ref)
>> >
>> >> sessionInfo()
>> > R version 2.15.0 Patched (2012-06-04 r59517)
>> > Platform: i686-pc-linux-gnu (32-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> > [7] LC_PAPER=C 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] Rsubread_1.6.3
>> >
>> >
>> > Regards,
>> > Dan
>> >
>> > On Tue, 2012-06-05 at 09:45 +0200, Robert Castelo wrote:
>> >> hi,
>> >>
>> >> the computer room at my university where we do practicals on R &
>> Bioconductor runs a 32bit linux distribution and when i tried to run
>> the latest version of the Rsubread package (1.6.3) it crashes when
>> calling the buildindex() function on a multifasta file with the yeast
>> genome. this does *not* happen under a 64bit linux distribution.
>> >>
>> >> i have verified that installing the version before (1.4.4) on the
>> current R 2.15 it also crashes (on the 32bit), but two versions
>> before, the 1.1.1, it does *not* and it works smoothly on this 32bit
>> linux distribution.
>> >>
>> >> i'm pasting below the output of using the 1.6.3 and 1.1.1 on R 2.15
>> where allChr.fa is the multifasta file with the yeast genome.
>> >>
>> >> so i can manage by now the problem by using the 1.1.1 version on R
>> 2.15 for my teaching but i wonder whether there would be some easy
>> solution for this, or even if it could be a symptom of something else
>> that the Rsubread developers should worry about. i know that using a
>> 32bit system nowadays is quite obsolete but this is what i got for
>> teaching :( and i would be happy to let my students play with the
>> latest version of Rsubread in the future.
>> >>
>> >>
>> >> thanks!!!
>> >> robert.
>> >>
>> >> ======================Rsubread 1.6.3 on R 2.15=======================
>> >>
>> >>> library(Rsubread)
>> >>> sessionInfo()
>> >> R version 2.15.0 (2012-03-30)
>> >> Platform: i686-pc-linux-gnu (32-bit)
>> >>
>> >> locale:
>> >> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>> >> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>> >> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>> >> [7] LC_PAPER=C LC_NAME=C
>> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>> >>
>> >> attached base packages:
>> >> [1] stats graphics grDevices utils datasets methods base
>> >>
>> >> other attached packages:
>> >> [1] Rsubread_1.6.3
>> >>
>> >>> buildindex(basename="subreadindex", reference="allChr.fa",
>> memory=2500)
>> >>
>> >> Building a base-space index.
>> >> Size of memory used=2500 MB
>> >> Base name of the built index = subreadindex
>> >>
>> >> *** caught segfault ***
>> >> address 0xdf670cc0, cause 'memory not mapped'
>> >>
>> >> Traceback:
>> >> 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv =
>> as.character(cmd), PACKAGE = "Rsubread")
>> >> 2: buildindex(basename = "subreadindex", reference = "allChr.fa",
>> memory = 2500)
>> >>
>> >> Possible actions:
>> >> 1: abort (with core dump, if enabled)
>> >> 2: normal R exit
>> >> 3: exit R without saving workspace
>> >> 4: exit R saving workspace
>> >> Selection:
>> >>
>> >>
>> >> ======================Rsubread 1.1.1 on R 2.15=======================
>> >>
>> >>> library(Rsubread)
>> >>> buildindex(basename="subreadindex", reference="allChr.fa",
>> memory=2500)
>> >>
>> >> Building the index in the base space.
>> >> Size of memory requested=2500 MB
>> >> Index base name = subreadindex
>> >> INDEX ITEMS PER PARTITION = 275940352
>> >>
>> >> completed=40.88%; time used=1.7s; rate=2955.1k bps/s; total=12m bps
>> completed=81.76%; time used=2.4s; rate=4111.8k
>> bps/s; total=12m bps
>> >> All the chromosome files are processed.
>> >> | Dumping index
>> [===========================================================>]
>> >> Index subreadindex is successfully built.
>> >>> sessionInfo()
>> >> R version 2.15.0 (2012-03-30)
>> >> Platform: i686-pc-linux-gnu (32-bit)
>> >>
>> >> locale:
>> >> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>> >> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>> >> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>> >> [7] LC_PAPER=C LC_NAME=C
>> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>> >>
>> >> attached base packages:
>> >> [1] stats graphics grDevices utils datasets methods base
>> >>
>> >> other attached packages:
>> >> [1] Rsubread_1.1.1
>> >>
>> >> _______________________________________________
>> >> 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
>> >
>> > _______________________________________________
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>>
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