On 17 December 2017 at 19:15, Baptiste Auguie wrote: | Hi, | | The CRAN maintainers recently informed me that my cda package now fails on | CRAN. The root cause seems to be this error: | | ** testing if installed package can be loaded | Error: package or namespace load failed for ‘cda’ in dyn.load(file, DLLpath | = DLLpath, ...): | unable to load shared object ‘/home/hornik/tmp/R.check/r- | release-gcc/Work/build/Packages/cda/libs/cda.so’: | /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/cda/libs/cda.so: | undefined symbol: zgbsv_ | | Google informs me that zgbsv is part of Lapack (specifically, a function to | solve a complex system of linear equations with 'banded matrices'). I | should note that I have not updated the package for quite a while, so this | breakage is likely occurring because of upstream changes in R or Rcpp or | RcppArmadillo or Armadillo (my guess).
All of the above only pass through to Lapack, and R is their only interface (in the use case of R packages we consider here). As you use complex variables (which is rare otherwise) this can bite _if_ the internal-to-R and incomplete Lapack system uses the internal copy which may not be complete. | I've encountered this type of problem at least twice in the past 5-6 years: | my package relies on Armadillo's C++ solve() function to solve a complex | linear system (not "banded" though, as far as I know), and Armadillo tends | to assume that a full Lapack is available, whereas R includes a subset. In Only if R is compiled / set-up to use the internal Lapack. For example the Debian and Ubuntu package generally are not. | the past the problem had occurred with zgels and zgesvx, and once before | that with zgetri. I was quite relieved when R Core added many Lapack | routines last year: | | https://github.com/wch/r-source/commit/98acd96f22eb795a933879c0d3f740 | e802855473 | | which solved (no pun intended) my problems. Dirk (Rcpp) and Conrad | (Armadillo) both agreed this was the best way forward. Unfortunately the | problem has resurfaced out of the blue with zgbsv, which is not on this | list. I'm left wondering: | | - what recent change could have caused my package to need this new routine | (if it is needed)? There was a recent NEWS item to this effect: CHANGES IN R 3.4.3 patched: NEW FEATURES: [...] • The version of LAPACK included in the sources has been updated to 3.8.0 (for the routines used by R a very minor bug-fix change). so this may be related. Dirk | - what would be a good way forward? In the past I tried adding the required | file from Netlib directly into my package, but that brings other issues | (unnecessary code duplication, especially if the code isn't even needed, | but also authorship changes, etc.) | | Thanks for any advice. | | Best regards, | | baptiste | | [[alternative HTML version deleted]] | | ______________________________________________ | R-package-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-package-devel -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
