Hi,
Continuing my exploration of SGSeq ;-) Ok, I got my analyzeFeatures() data using an annotation file and I am trying to move on to analyzeVariants(). I get the following errors if I try it:
> sgfc.var<-analyzeVariants(sgfc,maxnvariant=NA,cores=8)
Find segments...
Find variants...
Error: subscript contains NAs or out-of-bounds indices
In addition: There were 11 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In mclapply(geneIDs, findVariantsPerGene, g = g, maxnvariant = maxnvariant, ... :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
2: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
3: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
4: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
5: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
6: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
7: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
8: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
9: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
10: In mclapply(x, "[[", j, mc.cores = cores) :
scheduled cores 4 encountered errors in user code, all values of the jobs will be affected
11: In (S4Vectors:::coercerToClass(element.type))(v, ...) :
NAs introduced by coercion
Any inputs appreciated ;-)
Sylvain
Hi Leonard,
Here goes:
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SGSeq_1.6.11 SummarizedExperiment_1.2.3
[3] Biobase_2.32.0 Rsamtools_1.24.0
[5] Biostrings_2.40.2 XVector_0.12.1
[7] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[9] IRanges_2.6.1 S4Vectors_0.10.3
[11] BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] igraph_1.0.1 AnnotationDbi_1.34.4 magrittr_1.5
[4] zlibbioc_1.18.0 GenomicAlignments_1.8.4 BiocParallel_1.6.6
[7] tools_3.3.1 DBI_0.5-1 rtracklayer_1.32.2
[10] bitops_1.0-6 RCurl_1.95-4.8 biomaRt_2.28.0
[13] RUnit_0.4.31 RSQLite_1.0.0 GenomicFeatures_1.24.5
[16] XML_3.98-1.4