On 18 December 2018 at 22:13, Emmanuel Charpentier wrote: | Dear Dirk, | | Le mardi 18 décembre 2018 à 12:00 -0600, Dirk Eddelbuettel a écrit : | > Emmanuel, | > | > I ran this by Kurt Hornik (CC'ed) who is a Debian user too and one | > who | > updates frequently. He has hit the issue as well as says that it | > seems to | > stem from rstan | | It's more complicated than that. reinstalling rstan, or even Rcpp the | rstan, isn't sufficient to install brms.
There are more C++ parts than rstan and Rcpp. I would try to reinstall them. | > and that updating "everything" seems to fix it, | | I checked that by reinstalling Sage's R (3.4.4 ATM) an my whole slate | of 493-29=464 packages + updates). Takes about 93 minutes, but seems to | work. Well neither Kurt nor I suggested to update ~500 packages but if you're happy now, so be it. | I'll do that for my systemwide R installation. I'll yell if something | goes wrong, of course... | | > just as I | > suggested to you as "qualified guess". We have no idea yet whose ABI | > changed. | > | > With that I think we can close this as a bug against the r-base | > package. It | > appears to be a bystander here. | | Indeed (with the proviso that I want to see that with R 3.5.1...). | | But I wonder how many potential bystanders are in Debian, and what | measures should be taken to retrieve the real source of the problem. | | Do you thing I should file a bug against glibc ? No because we have no minimally reproducible issue here. It wasn't an r-base either (and I am still inclined to close this). You did the right thing to file it here: https://github.com/paul-buerkner/brms/issues/573 Until we know more it should stay there. BTW there you write 'running as root' -- don't do that. I added myself to group staff as it is the group on /usr/local/lib/R/site-library. Now I can (and do) runn eg littler's 'install.r' as me. Been doing that for years. To sum up, if a binary is in Debian itself chances are it gets updated when it needs to. When we install "outside of the distro package manager" directly from CRAN things like this can happen. Maybe it was glibc. Maybe it was a change in g++. Maybe it was something else. Paul was correct in pointing to CRAN and the positive test results there. When nothing changes the package remains happy... Best, Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
