Problems installing tidyverse

moomin · November 18, 2019, 1:59pm

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!

mara · November 18, 2019, 2:28pm

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

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)

moomin · November 22, 2019, 2:50pm

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"?

mara · November 22, 2019, 3:10pm

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'

system · December 2, 2019, 2:11pm

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