Kurt Hornik submitted a bug report to the gfortran maintainers yesterday, and yes, it seems to have a lot to do with this.
He and Brian Ripley have been able to pinpoint it to certain gfortran revisions (specifically gfortran-9 at least r268992, or gfortran-8 at least r269349), but we're lacking a simple test case. -pd > On 18 Apr 2019, at 07:53 , Benjamin Christoffersen <boenn...@gmail.com> wrote: > > Thanks for the quick reply. First a correction. I meant Ubuntu 18.04.2 > of course, sorry. > >> In short, you need to look more closely. > Is there a way to tell which BLAS and LAPACK is used on the Debian > machines on CRAN? I checked the "CRAN Package Check Flavors" page but > there is no information there regarding BLAS or LAPACK. > > I have tried to test the package with Atlas, OpenBlas, and the > reference implementation with gcc 7.3.0 and 8.2.0. It all worked > without any errors. > > It seems that gcc has changed since January from version 8.2.0 and > 7.3.0 to 8.3.0 on the tests on CRAN. Further, it is now Debian version > 8.3.0-2 instead of Debian 8.2.0-7 and Debian 7.3.0-29. I do not know > whether this can matter. > > Sincerely yours, > Benjamin Christoffersen > > > > > > > > Den ons. 17. apr. 2019 kl. 11.38 skrev Dirk Eddelbuettel <e...@debian.org>: >> >> >> On 17 April 2019 at 11:06, Benjamin Christoffersen wrote: >> | Since the start of April, I have gotten some errors on the Debian >> | machines on the check on CRAN for my package dynamichazard. The places >> | where I get the errors seems to come down to LAPACK's dtrtri routine. >> | I have tried to reproduce the error on Debian 18.04.2 with clang 8.0.0 >> | but I cannot reproduce them. >> | >> | The errors came suddenly and the tests passed before. I see similar >> | issues (I think) in the following package: >> | - RcppHMM >> | - BNPmix >> | - themetagenomics >> | - tidytext >> | - stm >> | >> | Any ideas what the error may be? Here is the relevant code parts for >> | one of the failed tests: >> | >> https://github.com/boennecd/dynamichazard/blob/c42105feea5e2d16a8d461b7c606245a743b3e0a/src/for_tests.cpp#L216 >> | >> https://github.com/boennecd/dynamichazard/blob/c42105feea5e2d16a8d461b7c606245a743b3e0a/src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp#L26 >> | >> https://github.com/boennecd/dynamichazard/blob/c42105feea5e2d16a8d461b7c606245a743b3e0a/src/BLAS_LAPACK/R_BLAS_LAPACK.cpp#L67 >> >> There are four or more different sources of LAPACK and BLAS on Debian as we >> (since the late 1990s !!) utilize the nature of the _interface_ allowing >> different packages to fill in. >> >> So there could be >> i) the R internal source with a partial library -- Fedora/CentOS use this >> but the Debian distro builds do not >> ii) "reference BLAS", external, unoptimized >> iii) OpenBLAS, the successor to Goto, parallel via multithreading >> iv) Atlas, "tuned" but not mulitthreading >> and more as eg Intel MKL via a quick script (see my blog). >> >> As a historical aside, and way-back-when, ii) earned us year's long growling >> from the direction of Oxfordshire because some early/old versions of LAPACK >> had bugs. But it cuts both ways: the external versions tend to be complete >> whereas what R ships with internally contains a subset -- and at least one >> (early) user of RcppArmadillo was bitten when R built from sources using >> defaults would not have the complex operations he needed. To R Core's credit >> these missing functions got filled in over the years. >> >> In short, you need to look more closely. On the Ubuntu 18.10 machine that I >> type this on, sessionInfo()'s second paragraph has >> >> Matrix products: default >> BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 >> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.3.so >> >> which IIRC is also the default (via some Debian/Ubuntu internal 'ordering' of >> the available alternatives). >> >> Hth, Dirk >> >> -- >> 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 -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel