Full transcript please; you're compiling from source. 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