Yes. I could not believe it. It took several minutes. Here is the tail end: ......... ......... installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/l ibrary/gmapR/libs ** R ** inst ** preparing package for lazy loading Creating a generic function from function ‘directory’ in package ‘gmapR’ Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (gmapR) * installing *source* package ‘sendmailR’ ... ** package ‘sendmailR’ successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (sendmailR) * installing *source* package ‘fail’ ... ** package ‘fail’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (fail) * installing *source* package ‘BatchJobs’ ... ** package ‘BatchJobs’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (BatchJobs) ........ 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   base    other attached packages: [1] VariantTools_1.4.5       VariantAnnotation_1.8.13 Rsamtools_1.14.3       [4] Biostrings_2.30.1        GenomicRanges_1.14.4    XVector_0.2.0          [7] IRanges_1.20.7           BiocGenerics_0.8.0      BiocInstaller_1.12.1   loaded via a namespace (and not attached):  [1] AnnotationDbi_1.24.0   BatchJobs_1.2         BBmisc_1.6            [4] Biobase_2.22.0         BiocParallel_0.4.1    biomaRt_2.18.0        [7] bitops_1.0-6           brew_1.0-6             BSgenome_1.30.0      [10] codetools_0.2-8        DBI_0.2-7             digest_0.6.4         [13] fail_1.2               foreach_1.4.2          GenomicFeatures_1.14.5 [16] gmapR_1.4.3            grid_3.0.3             iterators_1.0.7      [19] lattice_0.20-29        Matrix_1.1-3          plyr_1.8.1           [22] Rcpp_0.11.1            RCurl_1.95-4.1        RSQLite_0.11.4       [25] rtracklayer_1.22.7     sendmailR_1.1-2       stats4_3.0.3         [28] stringr_0.6.2          tools_3.0.3           XML_3.95-0.2         [31] zlibbioc_1.8.0       >  On Friday, May 30, 2014 2:41 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: Did you actually manage to build it (i.e., the dependency gmapR) from source on the Mac? On Fri, May 30, 2014 at 11:26 AM, Silav Bremos <silavb@yahoo.com> wrote: SUCCESS. Thanks Dan, why did I not think of that? > >I looked into VariantTools_1.6.1.tar.gz package at http://bioconductor.org/packages/release/bioc/html/VariantTools.html. >Strange that it does not contain source folder or makefile in it. > > > > > >On Friday, May 30, 2014 1:54 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > > > >----- Original Message ----- >> From: "Silav Bremos" <silavb@yahoo.com> >> To: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Quine [guest]" <guest@bioconductor.org> >> Cc: bioconductor@r-project.org, moocphil@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@fhcrc.org> >> wrote: >> >> >> >> Hi Quine, >> >> VariantTools is only supported on Linux. >> >> Dan >> >> >> ----- Original Message ----- >> > From: "Quine [guest]" < guest@bioconductor.org > >> > To: bioconductor@r-project.org , moocphil@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. >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >        [[alternative HTML version deleted]] > > > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]