Adrien FABRE
2020-May-13 01:01 UTC
[R] 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. -- Adrien Fabre ?cole d'?conomie de Paris/Paris School of Economics ? Universit? Paris 1 (R4-47) Page personnelle/Home page <http://sites.google.com/view/adrien-fabre> (+33/0)6.10.37.90.51 [[alternative HTML version deleted]]
Bert Gunter
2020-May-13 01:37 UTC
[R] Sometimes commands do not terminate after upgrading to R 4.0 and Ubuntu 20.04
Please, please, please ... RStudio is a wholly separate product from R. Post on their website if you think Rstudio has problems. And ubuntu concerns should be posted on r-sig-debian, not here! This list is about R programming issues (mostly). Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, May 12, 2020 at 6:07 PM Adrien FABRE <lesgrains at gmail.com> wrote:> > 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. > > -- > Adrien Fabre > > ?cole d'?conomie de Paris/Paris School of Economics ? Universit? Paris 1 > (R4-47) > > Page personnelle/Home page <http://sites.google.com/view/adrien-fabre> > (+33/0)6.10.37.90.51 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Eric Berger
2020-May-13 05:17 UTC
[R] Sometimes commands do not terminate after upgrading to R 4.0 and Ubuntu 20.04
Adrien, you posted this same item 3 days ago to this list. And someone responded to it. Why are you posting the identical thing again to this list? As Bert writes, you should post to the r-sig-debian list. Eric On Wed, May 13, 2020 at 4:38 AM Bert Gunter <bgunter.4567 at gmail.com> wrote:> Please, please, please ... RStudio is a wholly separate product from > R. Post on their website if you think Rstudio has problems. And ubuntu > concerns should be posted on r-sig-debian, not here! This list is > about R programming issues (mostly). > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along > and sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > On Tue, May 12, 2020 at 6:07 PM Adrien FABRE <lesgrains at gmail.com> wrote: > > > > 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. > > > > -- > > Adrien Fabre > > > > ?cole d'?conomie de Paris/Paris School of Economics ? Universit? Paris 1 > > (R4-47) > > > > Page personnelle/Home page <http://sites.google.com/view/adrien-fabre> > > (+33/0)6.10.37.90.51 > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]