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> 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> > *Sent:* 30 November 2016 13:51:05 > *To:* Rodriguez Martinez, Andrea > *Cc:* Vincent Carey; 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> 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> >> Sent: 30 November 2016 12:39:12 >> To: Rodriguez Martinez, Andrea >> Cc: 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>> 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.ro >> driguez-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> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel