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
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