On 17 May 2025 at 20:07, ravi wrote:
| Ivan and Dirk,
| Finally, finally, your mojo works!
| 1. I followed Ivan's suggestion. I ran bspm::enable() in a new R session.
Installed a package. The process seemed to use r2u. Again, I followed Ivan and
restored the following lines in the script:
| echo "suppressMessages(bspm::enable())" >> ${RHOME}/etc/Rprofile.site
| echo "options(bspm.version.check=FALSE)" >> ${RHOME}/etc/Rprofile.site
We had told to comment those out for one step, and of course implied to turn
them back on by removing the comment. We may have been insufficiently clear.
Oh well. Now you know.
| 2. I then ran
| sudo ./add_cranapt_noble.sh
Bad idea in the sense that a) you already ran it and b) these scripts are not
long / sophisticated enough to know to be robust to run N times in sequence.
The idea is to run them _precisely_ one time.
| Before doing this, I made the file executable as program (after right
clicking on the properties). After this, I was able to run the above command.
| 3. Now, the old error message about not being able to locate
python3-{dbus,gi,apt} did not appear.
| 4. In a fresh R session, I was able to install packages via r2u.
| 5. One final question. I seem to have read somewhere that r2u provides
| binaries for about 5000 packages. If a particular package is not in a list,
| will I get a message? How will I know?
No 5k was a previous attempt. r2u was always north of 20k. On the '24.04 aka
noble' laptop here:
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 24.10
Release: 24.10
Codename: oracular
$ apt-cache search r-cran-* | wc -l
23038
$ apt-cache search r-bioc-* | wc -l
492
$
Some come from the distro so it is a slight overcount. For the count of 'only
r2u' check the website, I post and update the numbers here.
| Thanks to you, Ivan. Thanks, Dirk, for your patient help.
Congratulations to you for persevering. I hope you enjoy r2u going forward.
Dirk
| Cheers, Ravi
|
| On Saturday, 17 May 2025 at 20:42:17 CEST, Dirk Eddelbuettel
<e...@debian.org> wrote:
|
|
|
|
|
|
| On 17 May 2025 at 21:18, Ivan Krylov via R-SIG-Debian wrote:
| | В Sat, 17 May 2025 17:17:09 +0000 (UTC)
| | ravi via R-SIG-Debian <r-sig-debian@r-project.org> пишет:
| |
| | > 7. Anyway, the bspm package has now been installed in
| | > /usr/local/lib/R/site-library. No namespace error is returned.
| |
| | Try running bspm::enable() in a fresh R session. After that, do calls
| | to install.packages() in the same R session go through r2u? If yes,
| | feel free to restore the lines "suppressMessages(bspm::enable())" and
| | "options(bspm.version.check=FALSE)" in ${RHOME}/etc/Rprofile.site. If
| | no, maybe the resulting error messages provide more of a hint.
|
|
| That's actually a good debugging step:
| - check if you can use r2u without bspm, ie try to run
| sudo apt install r-cran-digest
| or any other package with more depenendies
| - if that works try to see why involving bspm does create an issue
|
| As Ivan noted, it matters to re-enable bspm in /etc/R/Rprofile.site
|
| Dirk
|
| --
| dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
|
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian@r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
|
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
