[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Wed Nov 30 17:26:10 CET 2016
You are not set up to compile from source. Specifically, you're missing a
fortran compiler (gfortran)
On Wed, Nov 30, 2016 at 11:06 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martinez13 at imperial.ac.uk> wrote:
> This is all I get:
>
> > source("https://bioconductor.org/biocLite.R")
> Bioconductor version 3.5 (BiocInstaller 1.25.2), ?biocLite for help
> > biocLite("MWASTools")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.25.2), R Under development
> (unstable) (2016-10-26 r71594).
> Installing package(s) ‘MWASTools’
> also installing the dependencies ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4:
> cannot download all files
> Packages which are only available in source form, and may need compilation
> of C/C++/Fortran:
> ‘minqa’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘irlba’ ‘igraph’
> Do you want to attempt to install these from sources?
> y/n: y
> trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/
> mavericks/contrib/3.4/MWASTools_0.99.10.tgz'
> Content type 'application/x-gzip' length 2205892 bytes (2.1 MB)
> ==================================================
> downloaded 2.1 MB
>
>
> The downloaded binary packages are in
> /var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn/T//Rtmp79qF9E/downloaded_
> packages
> installing the source packages ‘minqa’, ‘RcppEigen’, ‘lme4’, ‘SparseM’,
> ‘pbkrtest’, ‘quantreg’, ‘irlba’, ‘car’, ‘igraph’
>
> trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
> Content type 'application/x-gzip' length 53548 bytes (52 KB)
> ==================================================
> downloaded 52 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.2.9.0.
> tar.gz'
> Content type 'application/x-gzip' length 1209128 bytes (1.2 MB)
> ==================================================
> downloaded 1.2 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-12.tar.gz'
> Content type 'application/x-gzip' length 3868402 bytes (3.7 MB)
> ==================================================
> downloaded 3.7 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.74.tar.gz'
> Content type 'application/x-gzip' length 737540 bytes (720 KB)
> ==================================================
> downloaded 720 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
> Content type 'application/x-gzip' length 165269 bytes (161 KB)
> ==================================================
> downloaded 161 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.29.tar.gz'
> Content type 'application/x-gzip' length 1722772 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> trying URL 'https://cran.rstudio.com/src/contrib/irlba_2.1.2.tar.gz'
> Content type 'application/x-gzip' length 218471 bytes (213 KB)
> ==================================================
> downloaded 213 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
> Content type 'application/x-gzip' length 622922 bytes (608 KB)
> ==================================================
> downloaded 608 KB
>
> trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz'
> Content type 'application/x-gzip' length 3328353 bytes (3.2 MB)
> ==================================================
> downloaded 3.2 MB
>
> * installing *source* package ‘minqa’ ...
> ** package ‘minqa’ successfully unpacked and MD5 sums checked
> ** libs
> gfortran-4.8 -fPIC -g -O2 -c altmov.f -o altmov.o
> make: gfortran-4.8: No such file or directory
> make: *** [altmov.o] Error 1
> ERROR: compilation failed for package ‘minqa’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/minqa’
> * installing *source* package ‘RcppEigen’ ...
> ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
> ** libs
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
> -I../inst/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppEigen.cpp -o
> RcppEigen.o
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
> -I../inst/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o
> RcppExports.o
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include"
> -I../inst/include -fPIC -Wall -mtune=core2 -g -O2 -c fastLm.cpp -o
> fastLm.o
> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -L/Library/Frameworks/R.framework/Resources/lib
> -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas
> -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran
> -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-
> apple-darwin13.0.0/4.8.2'
> ld: library not found for -lquadmath
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [RcppEigen.so] Error 1
> ERROR: compilation failed for package ‘RcppEigen’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/RcppEigen’
> * installing *source* package ‘SparseM’ ...
> ** package ‘SparseM’ successfully unpacked and MD5 sums checked
> ** libs
> gfortran-4.8 -fPIC -g -O2 -c bckslv.f -o bckslv.o
> make: gfortran-4.8: No such file or directory
> make: *** [bckslv.o] Error 1
> ERROR: compilation failed for package ‘SparseM’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/SparseM’
> * installing *source* package ‘irlba’ ...
> ** package ‘irlba’ successfully unpacked and MD5 sums checked
> ** libs
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Matrix/include"
> -fPIC -Wall -mtune=core2 -g -O2 -c irlb.c -o irlb.o
> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
> -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Matrix/include"
> -fPIC -Wall -mtune=core2 -g -O2 -c utility.c -o utility.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> irlba.so irlb.o utility.o -L/Library/Frameworks/R.framework/Resources/lib
> -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas
> -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran
> -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-
> apple-darwin13.0.0/4.8.2'
> ld: library not found for -lquadmath
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [irlba.so] Error 1
> ERROR: compilation failed for package ‘irlba’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/irlba’
> ERROR: dependencies ‘minqa’, ‘RcppEigen’ are not available for package
> ‘lme4’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/lme4’
> ERROR: dependency ‘SparseM’ is not available for package ‘quantreg’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/quantreg’
> ERROR: dependency ‘irlba’ is not available for package ‘igraph’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/igraph’
> ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/pbkrtest’
> ERROR: dependencies ‘pbkrtest’, ‘quantreg’ are not available for package
> ‘car’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/car’
>
> The downloaded source packages are in
> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn
> /T/Rtmp79qF9E/downloaded_packages’
> Old packages: 'mgcv'
> Update all/some/none? [a/s/n]:
> n
> Warning messages:
> 1: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘minqa’ had non-zero exit status
> 2: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘RcppEigen’ had non-zero exit status
> 3: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘SparseM’ had non-zero exit status
> 4: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘irlba’ had non-zero exit status
> 5: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘lme4’ had non-zero exit status
> 6: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘quantreg’ had non-zero exit status
> 7: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘igraph’ had non-zero exit status
> 8: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘pbkrtest’ had non-zero exit status
> 9: In install.packages(pkgs = doing, lib = lib, ...) :
> installation of package ‘car’ had non-zero exit status
>
> Thanks very much,
> Andrea
> ------------------------------
> *From:* Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
> *Sent:* 30 November 2016 13:51:05
> *To:* Rodriguez Martinez, Andrea
> *Cc:* Vincent Carey; bioc-devel at r-project.org
>
> *Subject:* Re: [Bioc-devel] problems installing cran dependencies with
> BioC devel in mac
>
> Full transcript please; you're compiling from source.
>
> 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.ro
>> driguez-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]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
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