[BioC] Cannot Install ‘VariantTools’ Package on Mac

[Dan Tenenbaum]

----- Original Message -----
> From: "Silav Bremos" <silavb at yahoo.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Quine [guest]" <guest at bioconductor.org>
> Cc: bioconductor at r-project.org, moocphil at yahoo.com
> Sent: Friday, May 30, 2014 10:50:32 AM
> Subject: Re: [BioC] Cannot Install ‘VariantTools’ Package on Mac
> 
> 
> 
> 
> Thanks Dan. Is it possible to get source folder and makefile and then
> compile it on Mac?
> This is the message I got:
> 
> 
> > biocLite("VariantTools")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R
> version 3.1.0.
> Installing package(s) 'VariantTools'
> 
> package ‘VariantTools’ is available as a source package but not as a
> binary
> 

You could ty 
biocLite("VariantTools", type="source")

but it is very unlikely to work.

Dan


> 
> 
> 
> 
> 
> 
> 
> On Friday, May 30, 2014 1:43 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> wrote:
> 
> 
> 
> Hi Quine,
> 
> VariantTools is only supported on Linux.
> 
> Dan
> 
> 
> ----- Original Message -----
> > From: "Quine [guest]" < guest at bioconductor.org >
> > To: bioconductor at r-project.org , moocphil at yahoo.com
> > Sent: Friday, May 30, 2014 10:40:06 AM
> > Subject: Cannot Install ‘VariantTools’ Package on Mac
> > 
> > Can someone please provide help on installing ‘VariantTools’
> > package on Mac? Output shown below:
> > 
> > -- output of sessionInfo():
> > 
> > > biocLite("VariantTools")
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R
> > version 3.1.0.
> > Installing package(s) 'VariantTools'
> > 
> > package ‘VariantTools’ is available as a source package but
> > not as a binary
> > 
> > Warning message:
> > package ‘VariantTools’ is not available (for R version 3.1.0)
> > 
> > > 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] org.Hs.eg.db_2.14.0
> > [2] RSQLite_0.11.4
> > [3] DBI_0.2-7
> > [4] VariantAnnotation_1.10.1
> > [5] Rsamtools_1.16.0
> > [6] Biostrings_2.32.0
> > [7] XVector_0.4.0
> > [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
> > [9] GenomicFeatures_1.16.1
> > [10] AnnotationDbi_1.26.0
> > [11] Biobase_2.24.0
> > [12] GenomicRanges_1.16.3
> > [13] GenomeInfoDb_1.0.2
> > [14] IRanges_1.22.7
> > [15] BiocGenerics_0.10.0
> > [16] BiocInstaller_1.14.2
> > 
> > loaded via a namespace (and not attached):
> > [1] BatchJobs_1.2 BBmisc_1.6
> > BiocParallel_0.6.1
> > [4] biomaRt_2.20.0 bitops_1.0-6 brew_1.0-6
> > [7] BSgenome_1.32.0 codetools_0.2-8 digest_0.6.4
> > [10] fail_1.2 foreach_1.4.2
> > GenomicAlignments_1.0.1
> > [13] iterators_1.0.7 plyr_1.8.1 Rcpp_0.11.1
> > [16] RCurl_1.95-4.1 rtracklayer_1.24.1 sendmailR_1.1-2
> > [19] stats4_3.1.0 stringr_0.6.2 tools_3.1.0
> > [22] XML_3.98-1.1 zlibbioc_1.10.0
> > > 
> > -------------------------------------------------------
> > 
> > --
> > Sent via the guest posting facility at bioconductor.org.
> > 
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