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).
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 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel