[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Sean Davis
seandavi at gmail.com
Wed Nov 30 22:20:58 CET 2016
> On Nov 30, 2016, at 4:13 PM, Martin Morgan <martin.morgan at roswellpark.org> wrote:
>
> 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/ <https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/>
I am not sure if it is supposed to be, but this directory is empty.
Sean
>
> ?
>
> 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
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
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>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
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>>>
>>>
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