[Bioc-devel] NAMESPACE problem in MacOS with VariantFiltering

Wed Jul 23 09:47:17 CEST 2014

hi Martin,

On 07/23/2014 01:36 AM, Martin Morgan wrote:
> 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 your VariantAnnotation was out of date.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.

i kept a copy of the folder with those devel packages giving the 
problem, so I tried what you suggest and you're right, 'biocValid()' 
warns what the problem is about. A couple of weeks ago I was tweaking 
myself the VariantAnnotation package and gave and installed a version i 
naively called it 1.11.99 (corresponding to a modified version of 1.11.5 
or so), but then of course now i realize that VariantAnnotation would 
not be updated to the latest 1.11.16. Rightly, 'biocValid()' prompts the 
message

* Packages too new for Bioconductor version 3.0'

                   Version
VariantAnnotation "1.11.99"
                   LibPath
VariantAnnotation 
"/Library/Frameworks/R.framework/Versions/3.1/Resources/develLibrary

downgrade with biocLite("VariantAnnotation")

'biocValid()' is great! :)

thanks!
robert.

> 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
>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550