[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

[Dan Tenenbaum]

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Maybe try with a fresh install of R? Or try reinstalling everything that's outdated with biocLite()?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