[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering
Martin Morgan
mtmorgan at fhcrc.org
Wed Jul 23 01:36:40 CEST 2014
On 7/22/2014 4:27 PM, Robert Castelo wrote:
> 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!!
Comparing your sessionInfo() with Dan's I would have guessed that the error
occurred when trying to load VariantAnnotation, probably because your
VariantAnnotation was out of date. Hopefully
BiocInstaller::biocValid()
would have diagnosed this.
Martin
>
> 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 outdated with biocLite()?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
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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