I am encountering problems with the goseq package. I did some analysis few months ago without any problems and I now need to reuse the script for another part of the project. So, I used exactly the same command lines with the new data but I get an error message when launching the
nullp function. So I tried to re-do my old analysis and I have now the same error.
Here is my commands and the error:
pwf.D1 = nullp(D1.vector, 'mm10', 'ensGene') Loading required package: rtracklayer Loading required package: GenomicRanges Can't find mm10/ensGene length data in genLenDataBase... Trying to download from UCSC. This might take a couple of minutes. Erreur dans value[[3L]](cond) : Length information for genome mm10 and gene ID ensGene is not available. You will have to specify bias.data manually. De plus : Messages d'avis : 1: package ‘rtracklayer’ was built under R version 3.1.3 2: package ‘GenomicRanges’ was built under R version 3.1.2
Here is the command I used few months ago with the comments during the analysis was running:
pwf.D1 = nullp(D1.vector, 'mm10', 'ensGene') #Loading required package: rtracklayer #Loading required package: GenomicRanges #Can't find mm10/ensGene length data in genLenDataBase... Trying to download from UCSC. #This might take a couple of minutes. #Message d'avis : #In pcls(G) : initial point very close to some inequality constraints
Because I updated my Bioconductor packages recently (I think I used goseq_1.16.2 before) and I am using an old R version (still the one for Snow Leopard), I am thinking that it could be a problem of version compatibility... Here is my
R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale:  fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  limma_3.22.7 rtracklayer_1.26.3 GenomicRanges_1.18.4 goseq_1.18.0 AnnotationDbi_1.28.2  GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0 Biobase_2.26.0 BiocGenerics_0.12.1  RSQLite_1.0.0 DBI_0.3.1 geneLenDataBase_1.1.1 BiasedUrn_1.06.1 loaded via a namespace (and not attached):  base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9 BiocParallel_1.0.3  biomaRt_2.22.0 Biostrings_2.34.1 bitops_1.0-6 brew_1.0-6  checkmate_1.5.3 codetools_0.2-11 colorspace_1.2-6 digest_0.6.8  fail_1.2 foreach_1.4.2 GenomicAlignments_1.2.2 GenomicFeatures_1.18.7  ggplot2_1.0.1 GO.db_3.0.0 grid_3.1.1 gtable_0.1.2  iterators_1.0.7 lattice_0.20-31 magrittr_1.5 MASS_7.3-40  Matrix_1.2-0 mgcv_1.8-6 munsell_0.4.2 nlme_3.1-120  plyr_1.8.2 proto_0.3-10 Rcpp_0.11.6 RCurl_1.95-4.6  reshape2_1.4.1 Rsamtools_1.18.3 scales_0.2.4 sendmailR_1.2-1  stringi_0.4-1 stringr_1.0.0 tools_3.1.1 XML_3.98-1.1  XVector_0.6.0 zlibbioc_1.12.0
So, does anyone has an idea of the origin of the problem? Should I have to reinstall a newer R version or just manually install goseq_1.16.2?
Thank you for your help.