Samuele Carcagno
2020-Apr-30 14:40 UTC
[R-sig-Debian] problem with `viridis` on Ubuntu 20.04
Il 30/04/20 03:39, Dirk Eddelbuettel ha scritto:> > On 30 April 2020 at 03:26, Samuele Carcagno wrote: > | I'm not familiar with the internals of `viridisLite`, so I'm not sure > | I'd be able to help there. I could open a bug report on the > | `viridisLite` repo and see if the author has suggestions on how to > | narrow down the issue. > > It would help if someone running Ubuntu 20.04 could reproduce. >after some further investigation I found out that the issue was related to some calls to the `solve` function in `make.rgb`, and indeed running `example(solve)` would hang my R session. After I changed the default BLAS with: sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu the problem disappeared. The BLAS output of `sessionInfo` now that `solve` is working is: Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 while before when `solve` was not working it was: Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 so it seems the issue is with the Ubuntu package `libopenblas0-pthread` and has nothing to do with R. I don't know why openblas-pthread was the default BLAS on my system. Thank you for your help. Best, Sam
Dirk Eddelbuettel
2020-Apr-30 15:01 UTC
[R-sig-Debian] problem with `viridis` on Ubuntu 20.04
On 30 April 2020 at 16:40, Samuele Carcagno wrote: | after some further investigation I found out that the issue was related | to some calls to the `solve` function in `make.rgb`, and indeed running | `example(solve)` would hang my R session. After I changed the default | BLAS with: | | sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu | | the problem disappeared. The BLAS output of `sessionInfo` now that | `solve` is working is: | | Matrix products: default | BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 | LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 | | while before when `solve` was not working it was: | | Matrix products: default | BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 | LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 | | so it seems the issue is with the Ubuntu package `libopenblas0-pthread` | and has nothing to do with R. I don't know why openblas-pthread was the | default BLAS on my system. That is most helpful! It could potentially affect lots of other users too. And on the aforementioned rocker/r-ubuntu:20.04 image, if upgrade to libopenblas-dev I get it too: root at d9a07e9f0e5f:/work# apt install libopenblas-dev Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libopenblas-pthread-dev libopenblas0 libopenblas0-pthread The following NEW packages will be installed: libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.7 MB of archives. After this operation, 153 MB of additional disk space will be used. Do you want to continue? [Y/n] and then 'example(solve)' hangs at sh8 <- solve(h8) Not good at all. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk Eddelbuettel
2020-Apr-30 15:11 UTC
[R-sig-Debian] problem with `viridis` on Ubuntu 20.04
On 30 April 2020 at 10:01, Dirk Eddelbuettel wrote: | | On 30 April 2020 at 16:40, Samuele Carcagno wrote: | | after some further investigation I found out that the issue was related | | to some calls to the `solve` function in `make.rgb`, and indeed running | | `example(solve)` would hang my R session. After I changed the default | | BLAS with: | | | | sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu | | | | the problem disappeared. The BLAS output of `sessionInfo` now that | | `solve` is working is: | | | | Matrix products: default | | BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 | | LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 | | | | while before when `solve` was not working it was: | | | | Matrix products: default | | BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 | | LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 | | | | so it seems the issue is with the Ubuntu package `libopenblas0-pthread` | | and has nothing to do with R. I don't know why openblas-pthread was the | | default BLAS on my system. | | That is most helpful! It could potentially affect lots of other users too. | | And on the aforementioned rocker/r-ubuntu:20.04 image, if upgrade to | libopenblas-dev I get it too: | | root at d9a07e9f0e5f:/work# apt install libopenblas-dev | Reading package lists... Done | Building dependency tree | Reading state information... Done | The following additional packages will be installed: | libopenblas-pthread-dev libopenblas0 libopenblas0-pthread | The following NEW packages will be installed: | libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread | 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. | Need to get 13.7 MB of archives. | After this operation, 153 MB of additional disk space will be used. | Do you want to continue? [Y/n] | | and then 'example(solve)' hangs at | | sh8 <- solve(h8) | | Not good at all. Same on Debian. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org