R help - May 2020 - Sometimes commands do not terminate after upgrading to R 4.0 and Ubuntu 20.04

I have upgraded R (from 3.6 to 4.0) and RStudio (from 1.1 to 1.2.5) a few
days ago, and Ubuntu from 18.04 to 20.04 yesterday.

Since then, R sometimes never terminates when executing certain commands:
ivreg (from package AER), summary (of a logit regression) and logitmfx
(from package mfx). Sometimes these commands run fine, but most of the time
I have to kill the process because R won't terminate the execution, even
when pressing the red Stop button in RStudio.

When I tried example('AER'), it worked fine. Then I re-installed the
package AER. It threw 10 warnings of type In readLines(file, skipNul TRUE) : 
cannot open compressed file
'/usr/lib/R/site-library/[package]/DESCRIPTION', probable reason 'No
such
file or directory' where [package] is abind, colorspace, dichromat... (but
not AER).

Since then example('AER') throws a warning: no help found for ?AER?.

I've removed and reinstalled R 4.0: it didn't help. Besides, the apt
purge
r-base* r-recommended r-cran-* threw a warning: dpkg: warning: while
removing r-base-core, directory '/usr/lib/R/site-library' not empty so
not
removed. Also, there was a bunch of Package [package] is not installed, so
not removed, including for [package] equal to r-cran-abind and the other
listed above (this purge also returned a bunch of Note, selecting [package]
for glob 'r-cran-*').

I have the same bug when using R from the terminal. For the record, I was
probably working on RStudio during the upgrade to Ubuntu 20.04. Also, I
can't recall if this issue started after I upgraded R and RStudio (which
would be my best guess) or after I upgraded Ubuntu (a day or two later).

I hope someone can help.

	[[alternative HTML version deleted]]

>>>>> "Adrien" == Adrien FABRE <lesgrains at
gmail.com> writes:
  Adrien> I have upgraded R (from 3.6 to 4.0) and RStudio (from 1.1 to 1.2.5)
a few
  Adrien> days ago, and Ubuntu from 18.04 to 20.04 yesterday.

  Adrien> Since then, R sometimes never terminates when executing certain
commands:
  Adrien> ivreg (from package AER), summary (of a logit regression) and
logitmfx
  Adrien> (from package mfx). Sometimes these commands run fine, but most of
the time
  Adrien> I have to kill the process because R won't terminate the
execution, even
  Adrien> when pressing the red Stop button in RStudio.

  Adrien> When I tried example('AER'), it worked fine. Then I
re-installed the
  Adrien> package AER. It threw 10 warnings of type In readLines(file,
skipNul   Adrien> TRUE) :  cannot open compressed file
  Adrien> '/usr/lib/R/site-library/[package]/DESCRIPTION', probable
reason 'No such
  Adrien> file or directory' where [package] is abind, colorspace,
dichromat... (but
  Adrien> not AER).

  Adrien> Since then example('AER') throws a warning: no help found
for ?AER?.

  Adrien> I've removed and reinstalled R 4.0: it didn't help.
Besides, the apt purge
  Adrien> r-base* r-recommended r-cran-* threw a warning: dpkg: warning:
while
  Adrien> removing r-base-core, directory '/usr/lib/R/site-library'
not empty so not
  Adrien> removed. Also, there was a bunch of Package [package] is not
installed, so
  Adrien> not removed, including for [package] equal to r-cran-abind and the
other
  Adrien> listed above (this purge also returned a bunch of Note, selecting
[package]
  Adrien> for glob 'r-cran-*').

  Adrien> I have the same bug when using R from the terminal. For the record,
I was
  Adrien> probably working on RStudio during the upgrade to Ubuntu 20.04.
Also, I
  Adrien> can't recall if this issue started after I upgraded R and
RStudio (which
  Adrien> would be my best guess) or after I upgraded Ubuntu (a day or two
later).

  Adrien> I hope someone can help.

There has been a discussion on R-SIG-Debian recently,
and /perhaps/ it is related to your troubles.

See https://stat.ethz.ch/pipermail/r-sig-debian/2020-April/003159.html
and in particular
https://stat.ethz.ch/pipermail/r-sig-debian/2020-April/003166.html
.


-- 
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net