[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>
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> 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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