[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source
Leonardo Collado Torres
lcoll@do @ending from jhu@edu
Sun Nov 4 19:01:04 CET 2018
Thanks for the info Kasper!
On Sun, Nov 4, 2018 at 11:28 AM Kasper Daniel Hansen
<kasperdanielhansen using 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 <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...)
>>
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