[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

hi Dan,

I re-installed R, getting the newer 3.1.1 over the 3.1.0 I had but did not make
a difference because I had the devel packages into a specific devel folder which
was still available to the installation. However, when I removed it and made a
completely new fresh installation of VariantFiltering and its dependencies then
it worked, so problem solved! thanks for the hint!!

robert.


On 7/22/14 9:11 PM, Dan Tenenbaum wrote:

Hi Robert,

I just installed VariantFiltering on my system (using the Snow Leopard build
of R) and had no trouble loading it.
Here's my sessionInfo():

R version 3.1.1 (2014-07-10)
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] VariantFiltering_1.1.9   BiocGenerics_0.11.3      BiocContributions_0.99.0
[4] BiocInstaller_1.15.5

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_3.1.1
[37] stringr_0.6.2                      tools_3.1.1
[39] VariantAnnotation_1.11.16          XML_3.98-1.1
[41] xtable_1.7-3                       XVector_0.5.7
[43] zlibbioc_1.11.1

Maybe try with a fresh install of R? Or try reinstalling everything that's
outdated with biocLite()?
Dan



----- Original Message -----

From: "Robert Castelo" <robert.castelo at upf.edu>
To: bioc-devel at r-project.org
Sent: Tuesday, July 22, 2014 11:25:51 AM
Subject: [Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

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