It is huge file, 14.5MB!
I think it was the size of the sequences. I tried it with a smaller
sequence set and it works fine.
Is there a limit on the input sequence size?

The EMBOSS infoseq output for the sequence file tmp.fasta is:
@>infoseq tmp.fasta
Display basic information about sequences
USA                      Database  Name           Accession      Type
Length %GC    Organism            Description
fasta::tmp.fasta:37668520-37776656 -              37668520-37776656 -
       N    *108136* 47.23
fasta::tmp.fasta:56850824-57028178 -              56850824-57028178 -
       N    *177354* 41.11
fasta::tmp.fasta:167225896-167251982 -              167225896-167251982 -
           N    *26086*  48.31
fasta::tmp.fasta:43298974-43304071 -              43298974-43304071 -
       N    *5097*   46.71
fasta::tmp.fasta:53625838-53795602 -              53625838-53795602 -
       N    *169764* 39.92
fasta::tmp.fasta:35820170-36757745 -              35820170-36757745 -
       N    *937575* 41.74

On Fri, Mar 29, 2013 at 2:08 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
> Keeping this on the list...
>
> On Fri, Mar 29, 2013 at 11:02 AM, Lakshmanan Iyer <liyer01@tufts.edu>
wrote:
>> Yhe commands are:
>>> library(rGADEM)
>>> library (BSgenome)
>>> library(BSgenome.Mmusculus.UCSC.mm9)
>>> Sequences <- readDNAStringSet ("./tmp.fasta", "fasta")
>>> gadem <- GADEM (Sequences, verbose=1, genome=Mmusculus)
>> *** Start C Programm ***
>> bit calloc failed!
>>
>
> Are you able to share the tmp.fasta file?
> Dan
>
>
>> On Wed, Mar 27, 2013 at 4:59 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
wrote:
>>> Hi,
>>>
>>>
>>> On Wed, Mar 27, 2013 at 1:53 PM, Lakshmanan Iyer <liyer01@tufts.edu>
wrote:
>>>> I am trying to rGADEM on a few sequences in FASTA format and it
>>>> crashes with the following error:
>>>>
>>>>> gadem <- GADEM (Sequences, verbose=1)
>>>
>>> Can you send the commands or data necessary to generate the Sequences
>>> object you are passing to GADEM()?
>>> Dan
>>>
>>>
>>>
>>>> *** Start C Programm ***
>>>> bit calloc failed!
>>>>
>>>> Any help appreciated!
>>>>> sessionInfo()
>>>> R version 2.15.0 (2012-03-30)
>>>> Platform: x86_64-pc-linux-gnu (64-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] grid      stats     graphics  grDevices utils     datasets  methods
>>>> [8] base
>>>>
>>>> other attached packages:
>>>> [1] rGADEM_2.6.0         seqLogo_1.24.0       BSgenome_1.26.1
>>>> [4] GenomicRanges_1.10.7 Biostrings_2.26.3    IRanges_1.16.6
>>>> [7] BiocGenerics_0.4.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] parallel_2.15.0 stats4_2.15.0
>>>>
>>>> -best
>>>> -Lax
>>>>
>>>> _______________________________________________
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