[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Wed Nov 30 14:51:05 CET 2016
Full transcript please; you're compiling from source.
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
>
>
>
>
>
>
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>
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