[BioC] Rsubread crashes in 32bit linux
Dan Du
tooyoung at gmail.com
Tue Jun 5 15:43:37 CEST 2012
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
>
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