[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

Wed Jul 23 01:27:20 CEST 2014

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 Maybe try with a fresh install of R? Or try reinstalling everything that's outdated with biocLite()?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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>>