[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

Robert Castelo robert.castelo at upf.edu
Tue Jul 22 20:25:51 CEST 2014


after updating to the last devel version of all packages I cannot load 
one of the packages I develop, VariantFiltering, in MacOS (Snow Leopard) 
while the same version loads smoothly in LInux.

This is the error I get:

No methods found in "IRanges" for requests: Rle, substring, ifelse, 
Error : object ‘runValue’ is not exported by 'namespace:IRanges'
Error: package or namespace load failed for ‘VariantFiltering’

You will find the sessionInfo() at the end of the email, the package 
version is the very last one as I can see from the installed package 

[1] "1.1.9"

which, as I said, loads without any trouble in my linux box. This last 
version 1.1.9 does not attempt to import the failed requests from 
IRanges and in fact the check report at


does not show any problem either. So I guess this problem may be 
specific of my Mac OS Snow Leopard installation and I'm really puzzled, 
any hint will be highly appreciated.

thank you!
ps: sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] BiocGenerics_0.11.3 vimcom_0.9-93 setwidth_1.0-3
[4] colorout_1.0-2

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.27.8 BatchJobs_1.3
[3] BBmisc_1.7 Biobase_2.25.0
[5] BiocParallel_0.7.7 biomaRt_2.21.1
[7] Biostrings_2.33.13 bitops_1.0-6
[9] brew_1.0-6 BSgenome_1.33.8
[11] BSgenome.Hsapiens.UCSC.hg19_1.3.99 caTools_1.17
[13] checkmate_1.1 codetools_0.2-8
[15] DBI_0.2-7 digest_0.6.4
[17] fail_1.2 foreach_1.4.2
[19] GenomeInfoDb_1.1.13 GenomicAlignments_1.1.22
[21] GenomicFeatures_1.17.12 GenomicRanges_1.17.26
[23] htmltools_0.2.4 httpuv_1.3.0
[25] IRanges_1.99.23 iterators_1.0.7
[27] Rcpp_0.11.2 RCurl_1.95-4.1
[29] RJSONIO_1.2-0.2 Rsamtools_1.17.31
[31] RSQLite_0.11.4 rtracklayer_1.25.13
[33] S4Vectors_0.1.2 sendmailR_1.1-2
[35] shiny_0.10.0 stats4_3.1.0
[37] stringr_0.6.2 tools_3.1.0
[39] XML_3.98-1.1 xtable_1.7-3
[41] XVector_0.5.7 zlibbioc_1.11.1

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