[R-sig-Debian] Sometimes commands do not terminate after upgrading to R 4.0 and Ubuntu 20.04

[Dirk Eddelbuettel]

Salut Adrien,

On 13 May 2020 at 14:19, Adrien FABRE 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 or doing Ctrl + C when using R
| in the terminal.
| 
| 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. I've downgraded to R
| 3.6: it didn't help. I've tried both answering yes or No when asked to
| install the packages in a personal library: none works. So I think the
| problem comes from Ubuntu 20.04, and is related to this post:
| https://stat.ethz.ch/pipermail/r-sig-debian/2020-April/003166.html. When I
| reinstall packages, I have a bunch of warnings related to Fortran 2018 that
| no longer support certain commands.
| 
| I hope someone can help.

Yes! See an email thread here started on the (Debian "internal" but of course
public) list debian-science by me on April 30 and carried into May
so you need both

  https://lists.debian.org/debian-science/2020/04/msg00081.html
  https://lists.debian.org/debian-science/2020/05/msg00000.html

as the thread spanse two months.

It appears to be a bad OpenMP and and OpenBLAS interaction you can (for now)
avoid) by replacing the 'pthread' variant of OpenBLAS with the OpenMP version
(see the thread for details).  Doing

  sudo apt install  libopenblas-openmp-dev
  sudo apt remove libopenblas-pthread-dev

should do -- make sure you do the second step too to ensure that the pthread
variant is remove as it would rank higher. Check via `R -s -e 'sessionInfo()'`
and look closely at the path printed for blas+lapack. Without pthread you
should be good.

Seb, CC'ed, and who is I have that right ma actually pretty close to you via
the PSE, is actually looking for someone with the proper hardware to create a
proper bug report. I was able to reproduce this once on my systems (both
Ubuntu and Debian testing) but was unable later. Some hardware dependence
still likely.

So in short: yes, we're aware, there is a workaround, but we could use help
in pinning it down. And sorry for the trouble. Apparently an old bug reborn.

Amicalement,  Dirk

PS Am a AMSE grad myself though it had a different name at the time ;-)
 
| -- 
| Adrien Fabre
| 
| École d'Économie de Paris/Paris School of Economics – Université 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-SIG-Debian mailing list
| R-SIG-Debian using r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org