Dirk, Thanks for the blog post on this, and the pointers in this email.
I have a question: it seems to me that you end up using a different compiler for the package (quantreg) than was used to build R itself. As I understand ABI changes, this is considered unsupported (ok, that depends on what version of gcc/gfortran was used to build R, but there has been a lot of ABI changes in GCC). Is that correct? I understand that this shortcut makes it much easier to use different compilers, and might work for Roger's usecase, but I was wondering about this issue of using a different compiler for packages. Is this something I should worry about? Best, Kasper On Sun, Aug 4, 2019 at 10:41 AM Dirk Eddelbuettel <e...@debian.org> wrote: > > Roger, > > On 4 August 2019 at 06:48, Koenker, Roger W wrote: > | I’d like to solicit some advice on a debugging problem I have in the > quantreg package. > | Kurt and Brian have reported to me that on Debian machines with gfortran > 9 > | > | library(quantreg) > | f = summary(rq(foodexp ~ income, data = engel, tau = 1:4/5)) > | plot(f) > | > | fails because summary() produces bogus estimates of the coefficient > bounds. > | This example has been around in my R package from the earliest days of > R, and > | before that in various incarnations of S. The culprit is apparently > rqbr.f which is > | even more ancient, but must have something that gfortran 9 doesn’t > approve of. > | > | I note that in R-devel there have been some other issues with gfortran > 9, but these seem > | unrelated to my problem. Not having access to a machine with an > R/gfortran9 > | configuration, I can’t apply my rudimentary debugging methods. I’ve > considered > | trying to build gfortran on my mac air and then building R from source, > but before > | going down this road, I wondered whether others had other suggestions, or > | advice about my proposed route. As far as I can see there are not yet > | binaries for gfortran 9 for osx. > > Maybe installing and running Docker on your mac is an alternative? > > Minimally viable example using > > a) docker (on Linux, but it is portable) and > > b) the current official 'r-base' container (an alias to our Rocker > r-base container) > > r-base is begged to Debian testing, and also allows you to get Debian > unstable. Below I fire up the container, tell it to use bash (not R) and > update > > edd@rob:~/git$ docker run --rm -ti r-base bash > root@1307193fadf4:/# > root@1307193fadf4:/# apt-get update > Get:1 http://cdn-fastly.deb.debian.org/debian sid InRelease [149 kB] > Get:2 http://cdn-fastly.deb.debian.org/debian testing InRelease [117 kB] > Get:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages > [8,385 kB] > Get:4 http://cdn-fastly.deb.debian.org/debian testing/main amd64 > Packages [7,918 kB] > Fetched 16.6 MB in 4s (4,649 kB/s) > Reading package lists... Done > root@1307193fadf4:/# apt-cache policy gcc-9 > gcc-9: > Installed: (none) > Candidate: 9.1.0-10 > Version table: > 9.1.0-10 990 > 990 http://deb.debian.org/debian testing/main amd64 Packages > 500 http://http.debian.net/debian sid/main amd64 Packages > root@1307193fadf4:/# apt-cache policy gfortran-9 > gfortran-9: > Installed: (none) > Candidate: 9.1.0-10 > Version table: > 9.1.0-10 990 > 990 http://deb.debian.org/debian testing/main amd64 Packages > 500 http://http.debian.net/debian sid/main amd64 Packages > root@1307193fadf4:/# > > At this point it just a matter of actually installing gcc-9 and gfortran-9 > (via apt-get install ...), and setting CC, FC, F77 and whichever other > environment variables the R build reflect to build quantreg. > > That said, this will be Debian's standard gfortran-9. What is at times a > little frustrating is that some of the builds used by some of the CRAN > tests > use local modifications which make their behaviour a little harder to > reproduce. I have an open issue with my (also old and stable) digest > package > which goes belly-up on a clang-on-Fedora build and nowhere else -- and I > have > been unable to reproduce this too. > > For such cases, having Docker container would be one possible way of > giving access to the test environment to make it accessible to more users. > > Best, Dirk > > > | > | Thanks, > | Roger > | > | Roger Koenker > | r.koen...@ucl.ac.uk<mailto:r.koen...@ucl.ac.uk> > | Department of Economics, UCL > | London WC1H 0AX. > | > | > | > | [[alternative HTML version deleted]] > | > | ______________________________________________ > | R-devel@r-project.org mailing list > | https://stat.ethz.ch/mailman/listinfo/r-devel > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Best, Kasper [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel