Quite frustrating. Any help would be appreciated.
I cannot install tidyverse, or any library, anymore. I am pasting a console log file from a install.packages() with some notes at the beginning of the file. I always get a non-zero exit status. I am running Microsoft R Open 3.5.0. I have reinstalled MS R Open 3.5 twice now with no luck. I am running R Studio 1.1.453
I know this is machine specify because I have no problems with my other machines.
MacOS High Sierra
Version 10.13.5
MacBook Air
Processor 1.7 GHz
Memory 8 GB
154.65 GB storage free
I am pasting interesting snippets from the console log file from a
install.packages("tidyverse", dependencies = TRUE)
separated with a "~~~~~~".
I always get a non-zero exit status. I am running Microsoft R Open 3.5.0. I have reinstalled MS R Open 3.5 twice now with no luck. I am running R Studio 1.1.453
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Multithreaded BLAS/LAPACK libraries detected. Using 2 cores for math algorithms.
Default CRAN mirror snapshot taken on 2018-06-01.
See: https://mran.microsoft.com/.
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
Reason: image not found
[Workspace loaded from ~/.RData]
> install.packages("tidyverse", dependencies = TRUE)
also installing the dependencies ‘colorspace’, ‘testthat’, ‘mnormt’, ‘munsell’, ‘processx’, ‘utf8’, ‘backports’, ‘plyr’, ‘psych’, ‘reshape2’, ‘bindrcpp’, ‘glue’, ‘Rcpp’, ‘tidyselect’, ‘digest’, ‘scales’, ‘lazyeval’, ‘mime’, ‘openssl’, ‘cellranger’, ‘callr’, ‘selectr’, ‘stringi’, ‘pillar’, ‘evaluate’, ‘markdown’, ‘yaml’, ‘htmltools’, ‘base64enc’, ‘rprojroot’, ‘broom’, ‘dplyr’, ‘dbplyr’, ‘forcats’, ‘ggplot2’, ‘haven’, ‘hms’, ‘httr’, ‘lubridate’, ‘modelr’, ‘purrr’, ‘readr’, ‘readxl’, ‘reprex’, ‘rlang’, ‘rvest’, ‘stringr’, ‘tibble’, ‘tidyr’, ‘xml2’, ‘feather’, ‘knitr’, ‘rmarkdown’
trying URL 'https://mran.microsoft.com/snapshot/2018-06-01/src/contrib/colorspace_1.3-2.tar.gz'
Content type 'application/octet-stream' length 293433 bytes (286 KB)
==================================================
downloaded 286 KB
~~~~~~
it downloads all the tar.gz with no problems
~~~~~~
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
Reason: image not found
* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** libs
/usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -fPIC -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -c colorspace.c -o colorspace.o
make: /usr/local/clang4/bin/clang: No such file or directory
make: *** [colorspace.o] Error 1
ERROR: compilation failed for package ‘colorspace’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/colorspace’
Warning in install.packages :
installation of package ‘colorspace’ had non-zero exit status
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
Reason: image not found
* installing *source* package ‘mnormt’ ...
** package ‘mnormt’ successfully unpacked and MD5 sums checked
** libs
gfortran -arch x86_64 -fPIC -g -O2 -c biv-nt.f -o biv-nt.o
make: gfortran: No such file or directory
make: *** [biv-nt.o] Error 1
ERROR: compilation failed for package ‘mnormt’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/mnormt’
Warning in install.packages :
installation of package ‘mnormt’ had non-zero exit status
Warning message:
From https://github.com/Homebrew/brew
* [new branch] master -> origin/master
HEAD is now at b87fc8c Merge pull request #4369 from MikeMcQuaid/cache_store_mkpath
==> Tapping homebrew/core
Cloning into '/private/var/folders/5n/1xj9jlpj2n9cxfbpfjf7ydbw0000gn/T/build-openssl@1.1/Library/Taps/homebrew/homebrew-core'...
Tapped 4579 formulae (4,831 files, 12.2MB)
Already up-to-date.
Error: Your Xcode (6.2) is too outdated.
Please update to Xcode 9.4 (or delete it).
Xcode can be updated from the App Store.
Using PKG_CFLAGS=-I/var/folders/5n/1xj9jlpj2n9cxfbpfjf7ydbw0000gn/T//build-openssl@1.1/opt/openssl@1.1/include -I/var/folders/5n/1xj9jlpj2n9cxfbpfjf7ydbw0000gn/T//build-openssl@1.1/opt/openssl/include
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
ERROR: dependencies ‘broom’, ‘dplyr’, ‘dbplyr’, ‘forcats’, ‘ggplot2’, ‘haven’, ‘hms’, ‘httr’, ‘lubridate’, ‘modelr’, ‘purrr’, ‘readr’, ‘readxl’, ‘reprex’, ‘rlang’, ‘rvest’, ‘stringr’, ‘tibble’, ‘tidyr’, ‘xml2’ are not available for package ‘tidyverse’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/tidyverse’
Warning in install.packages :
installation of package ‘tidyverse’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/5n/1xj9jlpj2n9cxfbpfjf7ydbw0000gn/T/RtmpFZs1Hw/downloaded_packages’
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library"