Thanks very much! ________________________________ From: Nitesh <nitesh.tur...@gmail.com> Sent: 30 November 2016 16:39:34 To: Rodriguez Martinez, Andrea; Kasper Daniel Hansen Cc: bioc-devel@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-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk>> wrote: Thanks very much for the clarification. Best wishes, Andrea ________________________________ From: Kasper Daniel Hansen <kasperdanielhan...@gmail.com<mailto:kasperdanielhan...@gmail.com>> Sent: 30 November 2016 16:26:10 To: Rodriguez Martinez, Andrea Cc: Vincent Carey; bioc-devel@r-project.org<mailto:bioc-devel@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-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk><mailto:andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@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 <kasperdanielhan...@gmail.com<mailto:kasperdanielhan...@gmail.com><mailto:kasperdanielhan...@gmail.com<mailto:kasperdanielhan...@gmail.com>>> Sent: 30 November 2016 13:51:05 To: Rodriguez Martinez, Andrea Cc: Vincent Carey; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@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-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk><mailto:andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@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 <st...@channing.harvard.edu<mailto:st...@channing.harvard.edu><mailto:st...@channing.harvard.edu<mailto:st...@channing.harvard.edu>>> Sent: 30 November 2016 12:39:12 To: Rodriguez Martinez, Andrea Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@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 <st...@channing.harvard.edu<mailto:st...@channing.harvard.edu><mailto:st...@channing.harvard.edu<mailto:st...@channing.harvard.edu>><mailto:st...@channing.harvard.edu<mailto:st...@channing.harvard.edu><mailto:st...@channing.harvard.edu<mailto:st...@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-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk><mailto:andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk>><mailto:andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk><mailto:andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@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@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>>> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Nitesh Turaga [[alternative HTML version deleted]]
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