Can't install tidyverse (and others) after upgrading to R 3.6

General
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1

Hello, I am a fairly novice R user but have been using 3.5.1 happily for some time. I upgraded to 3.6.2 last night, I also updated R Studio. I am running MacOS Mojave 10.14.6.

I set up a new library for 3.6 as this didnt happen automatically, updated my library paths and if I run .libPaths I get:
[1] "/Users/xxxxxxxxx/Library/R/3.6/library"
[2] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"

These libraries appear in my 'install packages' menu in R Studio. Most of my packages seem to have updated and reinstalled OK. I can wok with dplyr for example. However, tidyverse won't install.

I get the following error:

Installing package into ‘/Users/xxxxxxxxLibrary/R/3.6/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘broom’


  There is a binary version available but the source version is
  later:
      binary source needs_compilation
broom  0.5.3  0.5.4             FALSE

trying URL 'https://cran.ma.imperial.ac.uk/bin/macosx/el-capitan/contrib/3.6/tidyverse_1.3.0.tgz'
Content type 'application/x-gzip' length 433010 bytes (422 KB)
==================================================
downloaded 422 KB


The downloaded binary packages are in
	/var/folders/1_/wkz168ld00s6yp03mzzb7qjm0000gn/T//RtmprLXmRm/downloaded_packages
installing the source package ‘broom’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/broom_0.5.4.tar.gz'
Content type 'application/x-gzip' length 1228129 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘broom’
Execution halted
Warning in install.packages :
  installation of package ‘broom’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/1_/wkz168ld00s6yp03mzzb7qjm0000gn/T/RtmprLXmRm/downloaded_packages’

I have tried specifically installing broom and I get

There is a binary version available but the source version is
  later:
      binary source needs_compilation
broom  0.5.3  0.5.4             FALSE

installing the source package ‘broom’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/broom_0.5.4.tar.gz'
Content type 'application/x-gzip' length 1228129 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘broom’
Execution halted
Warning in install.packages :
  installation of package ‘broom’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/1_/wkz168ld00s6yp03mzzb7qjm0000gn/T/Rtmp32QR1a/downloaded_packages’

I was going to try using devtools to get from github but I have the same problem with the package 'callr' and cannot install devtools either. The packages I am aware of having an issue are: callr, broom, repr. There may be others.

I can see that broom was updated on 27 Jan so possibly there is a lag in the compiled version(?!) (I have seen other posters find that waiting a day solved it) - how likely is that?

I have unintsalled and reinstalled R studio, tried in the command line instead just to be thorough.

I tried downloading and unzipping broom direct into the library folder which worked briefly and the R studio kept crashing so this may have been foolhardy. Any help gratefully received.

2

Yes, there always is.

Once there is a binary version, compiling is no longer needed so installation is easier.

Compiling packages on macOS can be a nightmare, I recommend you to choose not to install from source when asked and wait for the binary version to update to the latest version.

3

Thank you so much. It now says needs_compilation = FALSE (yesterday it was TRUE) so I think this means that this is no longer the case. However I still cannot install (in fact the code above is from this morning when that was still the case). Have I understood correctly that the binary version is now updated? Or worth waiting longer?

I tried to go back to R3.5.3 (I was previously on 3.5.1 but was getting warnings for some of my packages) and now am in a nightmare of package updating with different issues. I wish I had listened to the warning voice in my head telling me not to update.....

4

There is still no binary available for the latest broom version, this usually takes some days, you just have to be patient. Why don't you just install the older binary version in the mean while?

This is something that has to be done sooner or later, at some point you will face a situation where you need to use a package that is only available for the latest R versions.

5

Thanks again, I will. I've got 3.5 up and running in the mean time so I can get on. I now feel slightly more confident that I will be able to manage the update in a few days.

I did try to install the older version but I think I needed devtools to do that and devtools was depending on callr so I ended up in a loop. It is no longer asking me the question re whether I want the old or new when I run install for broom.

6

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