[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

[Robert Castelo]

hi,

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:

library(VariantFiltering)
No methods found in "IRanges" for requests: Rle, substring, ifelse, 
as.factor
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 
description:

packageDescription("VariantFiltering")$Version
[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

http://www.bioconductor.org/checkResults/3.0/bioc-LATEST/VariantFiltering/perceval-checksrc.html

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

locale:
[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