Problems installing tidyverse

I'm using R studio version 3.3.3. I've been trying to install tidyverse but I've been having some issue. I've been trying to install tidyverse using:

install.packages("tidyverse")

when I do I receive this output

also installing the dependencies ‘ellipsis’, ‘rlang’, ‘vctrs’, ‘hms’


  There are binary versions available but the source versions are later:
          binary source needs_compilation
rlang      0.1.6  0.4.1              TRUE
hms        0.4.0  0.5.2             FALSE
tidyverse  1.1.1  1.2.1             FALSE

Do you want to install from sources the package which needs compilation?
y/n: 

Does anyone know what this means and what the correct input would be? It also asks an additional question and I've tried answering y to both but it just results in this and the package won't read using library():

Do you want to install from sources the package which needs compilation?
y/n: y
Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘ellipsis’ ‘vctrs’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘ellipsis’, ‘rlang’, ‘vctrs’, ‘hms’, ‘tidyverse’

trying URL 'https://cran.rstudio.com/src/contrib/ellipsis_0.3.0.tar.gz'
Content type 'application/x-gzip' length 7371 bytes
==================================================
downloaded 7371 bytes

trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.4.1.tar.gz'
Content type 'application/x-gzip' length 797012 bytes (778 KB)
==================================================
downloaded 778 KB

trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.2.0.tar.gz'
Content type 'application/x-gzip' length 668258 bytes (652 KB)
==================================================
downloaded 652 KB

trying URL 'https://cran.rstudio.com/src/contrib/hms_0.5.2.tar.gz'
Content type 'application/x-gzip' length 136186 bytes (132 KB)
==================================================
downloaded 132 KB

trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.2.1.tar.gz'
Content type 'application/x-gzip' length 61647 bytes (60 KB)
==================================================
downloaded 60 KB

Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
* 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/3.3/Resources/library/rlang’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rlang’
Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
* 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/3.3/Resources/library/ellipsis’
Warning in install.packages :
  installation of package ‘ellipsis’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘ellipsis’ is not available for package ‘vctrs’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/vctrs’
Warning in install.packages :
  installation of package ‘vctrs’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘vctrs’ is not available for package ‘hms’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/hms’
Warning in install.packages :
  installation of package ‘hms’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘hms’ is not available for package ‘tidyverse’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/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/5t/6clft5vx41dcn9cxxp220pq00000gn/T/RtmpwxNiUe/downloaded_packages’

Please let me know if you know what I can do to solve this or any other information that you might need to answer my question. Thank you!

This xcrun error means you're missing Xcode Command Line Tools and need to install them (I know, super obvious, right? :upside_down_face:)

The TL;DR solution is to run:
xcode-select --install
from the command line/terminal, but if you want more info...

Here's another post where the same happened (and I've got links in there)

1 Like

hello thank you.
I'm now receiving a different output but tidyverse is still failing to install. Now that I have Xcode command line tools installed it spits out a huge output that ends in:

installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/lubridate/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lubridate)
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
* installing *source* package ‘rvest’ ...
** package ‘rvest’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rvest)
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘vctrs’ is not available for package ‘hms’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/hms’
Warning in install.packages :
  installation of package ‘hms’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/pillar’
Warning in install.packages :
  installation of package ‘pillar’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
* installing *source* package ‘reprex’ ...
** package ‘reprex’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (reprex)
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘hms’ is not available for package ‘progress’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/progress’
Warning in install.packages :
  installation of package ‘progress’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘pillar’ is not available for package ‘tibble’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/tibble’
Warning in install.packages :
  installation of package ‘tibble’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘tibble’ is not available for package ‘dplyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/dplyr’
Warning in install.packages :
  installation of package ‘dplyr’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘tibble’ is not available for package ‘forcats’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/forcats’
Warning in install.packages :
  installation of package ‘forcats’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/ggplot2’
Warning in install.packages :
  installation of package ‘ggplot2’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘tibble’, ‘hms’ are not available for package ‘readr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/readr’
Warning in install.packages :
  installation of package ‘readr’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘tibble’, ‘progress’ are not available for package ‘readxl’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/readxl’
Warning in install.packages :
  installation of package ‘readxl’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘dplyr’, ‘tibble’ are not available for package ‘dbplyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/dbplyr’
Warning in install.packages :
  installation of package ‘dbplyr’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’ are not available for package ‘haven’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/haven’
Warning in install.packages :
  installation of package ‘haven’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘vctrs’ are not available for package ‘tidyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/tidyr’
Warning in install.packages :
  installation of package ‘tidyr’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘tidyr’ are not available for package ‘broom’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/broom’
Warning in install.packages :
  installation of package ‘broom’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘broom’, ‘dplyr’, ‘tibble’, ‘tidyr’ are not available for package ‘modelr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/modelr’
Warning in install.packages :
  installation of package ‘modelr’ had non-zero exit status
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'
ERROR: dependencies ‘broom’, ‘dbplyr’, ‘dplyr’, ‘forcats’, ‘ggplot2’, ‘haven’, ‘hms’, ‘modelr’, ‘pillar’, ‘readr’, ‘readxl’, ‘tibble’, ‘tidyr’ are not available for package ‘tidyverse’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status```

It still shows the same issue of the package having a "non-zero exit status"?

Hmm, it does look like there are several dependencies which failed to install, thus setting off more failures. Is there a reason you're using R 3.3? The current version is 3.6, and, unless you have a good reason not to, I'd highly recommend updating.
https://cloud.r-project.org/

The warning about strptime is strange, and not one I've seen before (after Googling it, seems like there was a bug that was taken care of in R 3.4.3):

Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Europe/London'

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