[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Martin Morgan
martin.morgan at roswellpark.org
Wed Nov 30 22:13:37 CET 2016
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/
?
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]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
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>>
>>
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