[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Sun Nov 4 17:27:45 CET 2018 

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 <lcollado using 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 using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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