----- Original Message ----- > From: "Sean Davis" <seand...@gmail.com> > To: "Martin Morgan" <martin.mor...@roswellpark.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Wednesday, November 30, 2016 1:20:58 PM > Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC > devel in mac
>> On Nov 30, 2016, at 4:13 PM, Martin Morgan <martin.mor...@roswellpark.org> >> wrote: >> >> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote: >>> Full transcript please; you're compiling from source. >> >> Excuse my ignorance about the Mac world but shouldn't these be available for >> binary installation via the URL Andrea provided, >> >> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/ >> <https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/> > > I am not sure if it is supposed to be, but this directory is empty. > Building binaries of packages for R-devel is not always CRAN's highest priority, but it could be worth asking about. Simon Urbanek is the Mac person at CRAN. Dan > Sean > > >> >> ? >> >> Martin >> >>> >>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea < >>> andrea.rodriguez-martine...@imperial.ac.uk> wrote: >>> >>>> Hi, >>>> >>>> >>>> Thanks for your reply. Maybe I am doing something wrong, but I do get >>>> errors, after I select the option install from source. See below: >>>> >>>> >>>>> source("https://bioconductor.org/biocLite.R") >>>>> biocLite("MWASTools") >>>> >>>> >>>> The downloaded source packages are in >>>> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn >>>> /T/Rtmp79qF9E/downloaded_packages’ >>>> Warning messages: >>>> 1: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘SparseM’ had non-zero exit status >>>> 2: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘irlba’ had non-zero exit status >>>> 3: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘minqa’ had non-zero exit status >>>> 4: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘RcppEigen’ had non-zero exit status >>>> 5: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘quantreg’ had non-zero exit status >>>> 6: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘lme4’ had non-zero exit status >>>> 7: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘pbkrtest’ had non-zero exit status >>>> 8: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘car’ had non-zero exit status >>>> 9: In install.packages(pkgs = doing, lib = lib, ...) : >>>> installation of package ‘igraph’ had non-zero exit status >>>> 10: In install.packages(update[instlib == l, "Package"], l, repos = >>>> repos, : >>>> installation of package ‘mgcv’ had non-zero exit status >>>> >>>> >>>>> sessionInfo() >>>> R Under development (unstable) (2016-10-26 r71594) >>>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>>> Running under: OS X El Capitan 10.11.6 >>>> >>>> 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] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] BiocInstaller_1.25.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tools_3.4.0 >>>> >>>> >>>> >>>> Thanks very much in advance, >>>> >>>> >>>> Best wishes, >>>> >>>> >>>> Andrea >>>> >>>> ________________________________ >>>> From: Vincent Carey <st...@channing.harvard.edu> >>>> Sent: 30 November 2016 12:39:12 >>>> To: Rodriguez Martinez, Andrea >>>> Cc: bioc-devel@r-project.org >>>> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC >>>> devel in mac >>>> >>>> In fact there was a problem installing igraph from source, but that is >>>> another issue. That can >>>> be resolved using the precompiled binary at http://igraph.org/r/#downloads >>>> >>>> >>>>> sessionInfo() >>>> >>>> R Under development (unstable) (2016-10-26 r71594) >>>> >>>> Platform: x86_64-apple-darwin13.4.0 (64-bit) >>>> >>>> Running under: OS X El Capitan 10.11.6 >>>> >>>> >>>> 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] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> other attached packages: >>>> >>>> [1] BiocInstaller_1.25.2 MWASTools_0.99.10 rmarkdown_1.1 >>>> >>>> >>>> loaded via a namespace (and not attached): >>>> >>>> [1] Rcpp_0.12.8 XVector_0.15.0 >>>> >>>> [3] GenomeInfoDb_1.11.6 nloptr_1.0.4 >>>> >>>> [5] ppcor_1.1 plyr_1.8.4 >>>> >>>> [7] zlibbioc_1.21.0 tools_3.4.0 >>>> >>>> [9] boot_1.3-18 digest_0.6.10 >>>> >>>> [11] lme4_1.1-12 evaluate_0.10 >>>> >>>> [13] tibble_1.2 gtable_0.2.0 >>>> >>>> [15] nlme_3.1-128 lattice_0.20-34 >>>> >>>> [17] mgcv_1.8-16 Matrix_1.2-7.1 >>>> >>>> [19] igraph_1.0.1 parallel_3.4.0 >>>> >>>> [21] SparseM_1.74 gridExtra_2.2.1 >>>> >>>> [23] stringr_1.1.0 IRanges_2.9.8 >>>> >>>> [25] S4Vectors_0.13.2 MatrixModels_0.4-1 >>>> >>>> [27] stats4_3.4.0 grid_3.4.0 >>>> >>>> [29] nnet_7.3-12 Biobase_2.35.0 >>>> >>>> [31] qvalue_2.7.0 minqa_1.2.4 >>>> >>>> [33] ggplot2_2.2.0 reshape2_1.4.2 >>>> >>>> [35] car_2.1-3 glm2_1.1.2 >>>> >>>> [37] magrittr_1.5 GenomicRanges_1.27.12 >>>> >>>> [39] scales_0.4.1 htmltools_0.3.5 >>>> >>>> [41] MASS_7.3-45 splines_3.4.0 >>>> >>>> [43] BiocGenerics_0.21.0 assertthat_0.1 >>>> >>>> [45] pbkrtest_0.4-6 SummarizedExperiment_1.5.3 >>>> >>>> [47] colorspace_1.3-1 quantreg_5.29 >>>> >>>> [49] stringi_1.1.2 lazyeval_0.2.0 >>>> >>>> [51] munsell_0.4.3 >>>> >>>> On Wed, Nov 30, 2016 at 7:27 AM, Vincent Carey <st...@channing.harvard.edu >>>> <mailto:st...@channing.harvard.edu>> wrote: >>>> sessionInfo()? I just did biocLite("MWASTools") with a devel version of >>>> R/BiocInstaller, >>>> and it seems to work well. >>>> >>>> On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea < >>>> andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea. >>>> rodriguez-martine...@imperial.ac.uk>> wrote: >>>> Hi, >>>> >>>> >>>> I'm trying to install my MWASTools package (devel branch) in mac, and I >>>> get a lot of errors regarding the installation of the dependencies from >>>> CRAN because there are no files in the repository: >>>> >>>> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/ >>>> >>>> >>>> For windows, I dont have any problems with the installation because the >>>> cran repository has the files: >>>> >>>> https://cran.rstudio.com/bin/windows/contrib/r-devel/ >>>> >>>> >>>> One solution, is to install the CRAN dependencies in advance using >>>> >>>>> install.packages(pkgs, contriburl = "https://cran.rstudio.com/bin/ >>>> macosx/mavericks/contrib/3.3/") >>>> >>>> >>>> I wonder if there is another solution to do this directly from biocLite. >>>> >>>> >>>> Thanks very much, >>>> >>>> >>>> Andrea >>>> >>>> >>>> >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> This email message may contain legally privileged and/or...{{dropped:2}} >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel