[Bioc-devel] problems installing cran dependencies with BioC devel in mac
Rodriguez Martinez, Andrea
andrea.rodriguez-martinez13 at imperial.ac.uk
Wed Nov 30 18:20:59 CET 2016
Thanks very much!
________________________________
From: Nitesh <nitesh.turaga at gmail.com>
Sent: 30 November 2016 16:39:34
To: Rodriguez Martinez, Andrea; Kasper Daniel Hansen
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac
This should help:
https://cran.r-project.org/bin/macosx/tools/
On Wed, 30 Nov 2016 at 11:29 Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at imperial.ac.uk<mailto:andrea.rodriguez-martinez13 at imperial.ac.uk>> wrote:
Thanks very much for the clarification.
Best wishes,
Andrea
________________________________
From: Kasper Daniel Hansen <kasperdanielhansen at gmail.com<mailto:kasperdanielhansen at gmail.com>>
Sent: 30 November 2016 16:26:10
To: Rodriguez Martinez, Andrea
Cc: Vincent Carey; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac
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<mailto:andrea.rodriguez-martinez13 at imperial.ac.uk><mailto:andrea.rodriguez-martinez13 at imperial.ac.uk<mailto: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<mailto:kasperdanielhansen at gmail.com><mailto:kasperdanielhansen at gmail.com<mailto:kasperdanielhansen at gmail.com>>>
Sent: 30 November 2016 13:51:05
To: Rodriguez Martinez, Andrea
Cc: Vincent Carey; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto: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<mailto:andrea.rodriguez-martinez13 at imperial.ac.uk><mailto:andrea.rodriguez-martinez13 at imperial.ac.uk<mailto: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<mailto:stvjc at channing.harvard.edu><mailto:stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>>>
Sent: 30 November 2016 12:39:12
To: Rodriguez Martinez, Andrea
Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org<mailto: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><mailto:stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>><mailto:stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu><mailto: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><mailto:andrea.rodriguez-martinez13 at imperial.ac.uk<mailto:andrea.rodriguez-martinez13 at imperial.ac.uk>><mailto:andrea.rodriguez-martinez13 at imperial.ac.uk<mailto:andrea.rodriguez-martinez13 at imperial.ac.uk><mailto: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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