[Bioc-devel] problems installing cran dependencies with BioC devel in mac
On Nov 30, 2016, at 4:13 PM, Martin Morgan <martin.morgan at 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-martinez13 at 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 <stvjc at channing.harvard.edu> Sent: 30 November 2016 12:39:12 To: Rodriguez Martinez, Andrea Cc: bioc-devel at 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 <stvjc at channing.harvard.edu <mailto:stvjc at 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-martinez13 at imperial.ac.uk<mailto:andrea. rodriguez-martinez13 at 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 at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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