Thanks for the info Kasper! On Sun, Nov 4, 2018 at 11:28 AM Kasper Daniel Hansen <kasperdanielhan...@gmail.com> wrote: > > You seem to install the Beta version of the Command Line tools. That's not > right. Look at the top of > apple.com/developer/downloads > (First try with xcode-select --install on the command line, which I could not > get to work).
I also tried that command and it didn't work for me either. > > Following installation of these tools you need to run the following command > which can be found in the R-admin manual (devel version of R, not the rebased > version) > https://cran.r-project.org/doc/manuals/r-devel/R-admin.html Ahh, I didn't know about this section of the manual. Thanks! > in section C.3: > > sudo installer -pkg \ > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > -target / > > On Fri, Nov 2, 2018 at 4:05 PM Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> Hi, >> >> I was about to send the email below, but eventually I got it to work. >> I'm sharing it anyway since others might run into similar issues. >> >> Basically, I needed the latest macOS command line tools installed, but >> getting them installed was tricky. I installed Xcode 10.1 (10B61) from >> the Mac App Store, then installed a version of the command line tools >> via >> https://download.developer.apple.com/Developer_Tools/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2.dmg, >> rebooted, then under "settings", "software update" detected that there >> was a newer version. Finally, I was then able to install the backports >> R package. >> >> Best, >> Leo >> >> >> >> ## Successful install: >> >> > install.packages('backports') >> Warning: unable to access index for repository >> https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6: >> cannot open URL >> 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES' >> Package which is only available in source form, and may need >> compilation of C/C++/Fortran: ‘backports’ >> Do you want to attempt to install these from sources? (Yes/no/cancel) y >> installing the source package ‘backports’ >> >> trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.2.tar.gz' >> Content type 'application/x-gzip' length 10900 bytes (10 KB) >> ================================================== >> downloaded 10 KB >> >> * installing *source* package ‘backports’ ... >> ** package ‘backports’ successfully unpacked and MD5 sums checked >> ** libs >> /usr/local/clang4/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/include -fPIC -Wall -g -O2 -c dotsElt.c -o dotsElt.o >> /usr/local/clang4/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/include -fPIC -Wall -g -O2 -c dotsLength.c -o >> dotsLength.o >> /usr/local/clang4/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o >> /usr/local/clang4/bin/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/clang4/lib -o backports.so dotsElt.o dotsLength.o init.o >> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework >> -Wl,CoreFoundation >> ld: warning: text-based stub file >> /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd >> and library file >> /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation >> are out of sync. Falling back to library file for linking. >> installing to >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/backports/libs >> ** R >> ** byte-compile and prepare package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> Loading required package: colorout >> devtools::install_github("jalvesaq/colorout") >> Warning message: >> In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, : >> there is no package called ‘colorout’ >> * DONE (backports) >> >> The downloaded source packages are in >> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/RtmpBZUipc/downloaded_packages’ >> > >> > sessionInfo() >> R Under development (unstable) (2018-04-05 r74542) >> Platform: x86_64-apple-darwin15.6.0 (64-bit) >> Running under: macOS 10.14.1 >> >> Matrix products: default >> BLAS: >> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib >> LAPACK: >> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib >> >> 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 >> >> loaded via a namespace (and not attached): >> [1] compiler_3.6.0 tools_3.6.0 tcltk_3.6.0 >> >> >> >> >> >> >> >> ## Older email: >> >> >> >> >> Hi, >> >> With Bioconductor 3.9 now being live, I got a few emails about some of >> my packages which I wanted to look into. For that I tried installing R >> 3.6 with all my current R 3.5 packages. I quickly ran into problems >> trying to install devtools. Basically, the backports package is not >> available as a binary and the compilation from source fails because it >> can't find an stdlib.h file. I also recently updated my Mac with the >> new OS as well as the latest Xcode (which in theory now comes with the >> command line tools that should include that stdlib.h file). I also >> installed the latest command line tools but still ran into the same >> issue. >> >> Has anyone else seen this issue and resolved it? If so, what step and I >> missing? >> >> Thanks, >> Leo >> >> >> > install.packages('backports') >> Warning: unable to access index for repository >> https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6: >> cannot open URL >> 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES' >> Package which is only available in source form, and may need >> compilation of C/C++/Fortran: ‘backports’ >> Do you want to attempt to install these from sources? (Yes/no/cancel) y >> installing the source package ‘backports’ >> >> trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.2.tar.gz' >> Content type 'application/x-gzip' length 10900 bytes (10 KB) >> ================================================== >> downloaded 10 KB >> >> * installing *source* package ‘backports’ ... >> ** package ‘backports’ successfully unpacked and MD5 sums checked >> ** libs >> /usr/local/clang4/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/include -fPIC -Wall -g -O2 -c dotsElt.c -o dotsElt.o >> In file included from dotsElt.c:1: >> /Library/Frameworks/R.framework/Resources/include/R.h:55:11: fatal >> error: 'stdlib.h' file not found >> # include <stdlib.h> /* Not used by R itself, but widely assumed in packages >> */ >> ^~~~~~~~~~ >> 1 error generated. >> make: *** [dotsElt.o] Error 1 >> ERROR: compilation failed for package ‘backports’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/backports’ >> >> The downloaded source packages are in >> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T/Rtmp2hfmV8/downloaded_packages’ >> Warning message: >> In install.packages("backports") : >> installation of package ‘backports’ had non-zero exit status >> > >> > sessionInfo() >> R Under development (unstable) (2018-04-05 r74542) >> Platform: x86_64-apple-darwin15.6.0 (64-bit) >> Running under: macOS 10.14.1 >> >> Matrix products: default >> BLAS: >> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib >> LAPACK: >> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib >> >> 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 >> >> loaded via a namespace (and not attached): >> [1] compiler_3.6.0 tools_3.6.0 tcltk_3.6.0 >> >> https://github.com/catboost/catboost/issues/137 lead me to >> https://forums.developer.apple.com/thread/104296 and searching for >> "macOS_SDK_headers_for_macOS_10.14. pkg" lead me to >> https://stackoverflow.com/questions/51274905/brew-install-on-mojave >> From https://developer.apple.com/download/more/ I downloaded and >> installed >> https://download.developer.apple.com/Developer_Tools/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2/Command_Line_Tools_macOS_10.14_for_Xcode_10.1_Beta_2.dmg >> >> I also ran the following: >> >> $ brew update >> $ brew doctor >> ## Plus some things that brew doctor recommended (that don't have >> anything to do with stdlib.h) >> $ brew upgrade gcc >> ==> Upgrading 1 outdated package: >> gcc 6.2.0 -> 8.2.0 >> ## more output deleted >> >> Ohhhhh, now "Software Update" is noticing a new Command Line Tools >> version. (and then that's when it worked...) >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
