[BioC] Rsubread crashes in 32bit linux

[Robert Castelo]

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