[Bioc-devel] problems installing cran dependencies with BioC devel in mac

Wed Nov 30 14:24:01 CET 2016

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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