On 6 July 2018 at 12:31, Enrico Schumann wrote: | Just as one more datapoint: I cannot reproduce the segfault, with | R 3.5.1 on (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not | build from source.) I have been a little too busy and have not yet upgraded to 18.04 so I can't attempt to replicate -- but it _looks_ just like a garden variety binary mismatch. We _know_ R 3.5.* requires _all_ binary packages to be reinstalled and it is easy to miss one. So unless G?ran shows us a generally reproducible bug I will suspect that this is simply a local deployment issue. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Den 2018-07-06 kl. 16:28, skrev Dirk Eddelbuettel:> > On 6 July 2018 at 12:31, Enrico Schumann wrote: | Just as one more > datapoint: I cannot reproduce the segfault, with | R 3.5.1 on > (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not | build > from source.) > > I have been a little too busy and have not yet upgraded to 18.04 so I > can't attempt to replicate -- but it _looks_ just like a garden > variety binary mismatch. > > We _know_ R 3.5.* requires _all_ binary packages to be reinstalled > and it is easy to miss one. So unless G?ran shows us a generally > reproducible bug I will suspect that this is simply a local > deployment issue.I suspect that too, since the segfault does _not_ occur if run R via RStudio. _But_, I have run 'update.packages(checkBuilt = TRUE)', and that should take care of reinstalling, right? Maybe it somehow is an issue with devtools::install_github. G?ran> Dirk >
On Fri, Jul 6, 2018 at 8:18 AM G?ran Brostr?m <goran.brostrom at umu.se> wrote:> > > > Den 2018-07-06 kl. 16:28, skrev Dirk Eddelbuettel: > > > > On 6 July 2018 at 12:31, Enrico Schumann wrote: | Just as one more > > datapoint: I cannot reproduce the segfault, with | R 3.5.1 on > > (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not | build > > from source.) > > > > I have been a little too busy and have not yet upgraded to 18.04 so I > > can't attempt to replicate -- but it _looks_ just like a garden > > variety binary mismatch. > > > > We _know_ R 3.5.* requires _all_ binary packages to be reinstalled > > and it is easy to miss one. So unless G?ran shows us a generally > > reproducible bug I will suspect that this is simply a local > > deployment issue. > > I suspect that too, since the segfault does _not_ occur if run R via > RStudio. _But_, I have run 'update.packages(checkBuilt = TRUE)', and > that should take care of reinstalling, right? > > Maybe it somehow is an issue with devtools::install_github.If you follow the error traceback (from the bottom of the stack to the top), the most recent package involved is 'curl'. It appears that the segfault occurs when it is loaded. You probably get the same if you attempt: library(curl) in a fresh R session. If so, as Dirk suggests:> We _know_ R 3.5.* requires _all_ binary packages to be reinstalled > and it is easy to miss one.make sure to reinstall 'curl'. If that solves it, it's likely that other packages have the same issue, so you probably want to start from a clean slate and wipe your current package library, e.g. unlink(.libPaths()[1], recursive = TRUE). /Henrik> > G?ran > > > Dirk > > > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
On 6 July 2018 at 17:18, G?ran Brostr?m wrote: | I suspect that too, since the segfault does _not_ occur if run R via | RStudio. _But_, I have run 'update.packages(checkBuilt = TRUE)', and | that should take care of reinstalling, right? That will catch all packages from _source code_ repositories. | Maybe it somehow is an issue with devtools::install_github. Well of course. `install_github` is "cowboy mode" which I argued against til I was blue in the face, but what can you do. Little, apart from using a drat repo instead. So there is your self-inflicted wound, and Henrik also showed you the trail back to curl. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org