Hi, Im a beginning to R, I only took one class back in 2018.
Im running version 1.1423 2009-2018 Rstudio on my mac.
I'm only using R to make a few plots of my data (violin plot W box plot overlay) but cant seem to get past package install and library steps.
These are the various installs I tried and every package I try to install give the same warning that the install had a non-zero exit status.
install.packages("tidyverse", repo = 'https://mac.R-project.org')
install.packages("tidyverse", dependencies = TRUE)
install.packages( "Rcpp", type = "source" )
install.packages( "dplyr" )
Here are the errors:
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
- installing source package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘fs’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/fs’
Warning in install.packages :
installation of package ‘fs’ had non-zero exit status - installing source package ‘rex’ ...
** package ‘rex’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (rex)
- installing source package ‘brio’ ...
** package ‘brio’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘brio’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/brio’
Warning in install.packages :
installation of package ‘brio’ had non-zero exit status - installing source package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘ps’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ps’
Warning in install.packages :
installation of package ‘ps’ had non-zero exit status - installing source package ‘lubridate’ ...
** package ‘lubridate’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘lubridate’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/lubridate’
Warning in install.packages :
installation of package ‘lubridate’ had non-zero exit status - installing source package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘rlang’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rlang’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status - installing source package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Found pkg-config cflags and libs!
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing: - deb: libxml2-dev (Debian, Ubuntu, etc)
- rpm: libxml2-devel (Fedora, CentOS, RHEL)
- csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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 ‘xml2’
- removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status - installing source package ‘ellipsis’ ...
** package ‘ellipsis’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘ellipsis’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ellipsis’
Warning in install.packages :
installation of package ‘ellipsis’ had non-zero exit status - installing source package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘xfun’ 0.4 is being loaded, but >= 0.19 is required
ERROR: lazy loading failed for package ‘knitr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/knitr’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/knitr’
Warning in install.packages :
installation of package ‘knitr’ had non-zero exit status
ERROR: dependency ‘ps’ is not available for package ‘processx’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
ERROR: dependency ‘openssl’ is not available for package ‘httr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status - installing source package ‘purrr’ ...
** package ‘purrr’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘purrr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/purrr’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/purrr’
Warning in install.packages :
installation of package ‘purrr’ had non-zero exit status
ERROR: dependency ‘ellipsis’ is not available for package ‘vctrs’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/vctrs’
Warning in install.packages :
installation of package ‘vctrs’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘callr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/callr’
Warning in install.packages :
installation of package ‘callr’ had non-zero exit status
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rvest’
Warning in install.packages :
installation of package ‘rvest’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘covr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/covr’
Warning in install.packages :
installation of package ‘covr’ had non-zero exit status
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pkgbuild’
Warning in install.packages :
installation of package ‘pkgbuild’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘vctrs’ are not available for package ‘tidyselect’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tidyselect’
Warning in install.packages :
installation of package ‘tidyselect’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘vctrs’ are not available for package ‘hms’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/hms’
Warning in install.packages :
installation of package ‘hms’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘vctrs’ are not available for package ‘pillar’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pillar’
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘fs’ are not available for package ‘reprex’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reprex’
Warning in install.packages :
installation of package ‘reprex’ had non-zero exit status
ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘pillar’, ‘vctrs’ are not available for package ‘tibble’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tibble’
Warning in install.packages :
installation of package ‘tibble’ had non-zero exit status
ERROR: dependency ‘tibble’ is not available for package ‘rematch2’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rematch2’
Warning in install.packages :
installation of package ‘rematch2’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘dplyr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘tibble’ are not available for package ‘forcats’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/forcats’
Warning in install.packages :
installation of package ‘forcats’ had non-zero exit status
ERROR: dependencies ‘hms’, ‘tibble’ are not available for package ‘readr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/readr’
Warning in install.packages :
installation of package ‘readr’ had non-zero exit status
ERROR: dependencies ‘diffobj’, ‘rematch2’, ‘tibble’ are not available for package ‘waldo’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/waldo’
Warning in install.packages :
installation of package ‘waldo’ had non-zero exit status
ERROR: dependencies ‘dplyr’, ‘ellipsis’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘dbplyr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/dbplyr’
Warning in install.packages :
installation of package ‘dbplyr’ had non-zero exit status
ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘haven’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/haven’
Warning in install.packages :
installation of package ‘haven’ had non-zero exit status
ERROR: dependencies ‘dplyr’, ‘ellipsis’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tidyr’
Warning in install.packages :
installation of package ‘tidyr’ had non-zero exit status
ERROR: dependencies ‘dplyr’, ‘ellipsis’, ‘tibble’, ‘tidyr’ are not available for package ‘broom’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/broom’
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
ERROR: dependencies ‘brio’, ‘callr’, ‘ellipsis’, ‘pkgload’, ‘processx’, ‘ps’, ‘waldo’ are not available for package ‘testthat’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/testthat’
Warning in install.packages :
installation of package ‘testthat’ had non-zero exit status
ERROR: dependency ‘testthat’ is not available for package ‘isoband’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependencies ‘broom’, ‘tibble’, ‘tidyr’, ‘tidyselect’, ‘vctrs’ are not available for package ‘modelr’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/modelr’
Warning in install.packages :
installation of package ‘modelr’ had non-zero exit status
ERROR: dependencies ‘isoband’, ‘tibble’ are not available for package ‘ggplot2’ - removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/7k/b3qpndxj42v4ms4rgs1nnj200000gn/T/RtmpFOu2HS/downloaded_packages’