> 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. 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