rGADEM bit calloc error
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@emiliomastriani-9776
Last seen 5.8 years ago

Hi guys,

I have the following problem running rGADEM on my fasta file. The error is very strange because I already used rGADEM on a very similar file (containing 1 sequence more, but bigger file size) successfully. 

Here you can find all information.

 

Best regards,

Emilio

> sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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=en_US.UTF-8       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      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] rGADEM_2.18.0        seqLogo_1.36.0       BSgenome_1.38.0     
 [4] rtracklayer_1.30.2   GenomicRanges_1.22.4 GenomeInfoDb_1.6.3  
 [7] Biostrings_2.38.4    XVector_0.10.0       IRanges_2.4.7       
[10] S4Vectors_0.8.11     BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] zlibbioc_1.16.0            GenomicAlignments_1.6.3   
 [3] BiocParallel_1.4.3         tools_3.2.3               
 [5] SummarizedExperiment_1.0.2 Biobase_2.30.0            
 [7] lambda.r_1.1.7             futile.logger_1.4.1       
 [9] futile.options_1.0.0       bitops_1.0-6              
[11] RCurl_1.95-4.7             Rsamtools_1.22.0          
[13] XML_3.98-1.3              
> Sequences
  A DNAStringSet instance of length 45
       width seq                                            names               
 [1] 3208674 TACTGCACGCTGAGGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_003197
 [2] 3208674 TACTGCGTACTGATGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_006905
 [3] 3208674 TACTGCACGCTGATGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_011083
 [4] 3208674 TACTGCACGCTGAGGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_011205
 [5] 3208674 TACTGCACGCTGACCCGTAACG...TTACGAAAACTGTCCTTAACG NC_015761
 ...     ... ...
[41] 3208674 TACTGCACGCTGAGGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_020307
[42] 3208674 TACTGCACGCTGATGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_021812
[43] 3208674 TACTGCACGCTGATGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_021844
[44] 3208674 TACTGCACGCTGAGGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_022221
[45] 3208674 TACTGCACGCTGAGGCGCAGCG...TTACGAAAACGGTCCTTAACG NC_022569
> gadem<-GADEM(Sequences,verbose=1)
*** Start C Programm ***
Error in GADEM(Sequences, verbose = 1) : bit calloc failed!

 

rGADEM • 689 views
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