Den 2017-12-01 kl. 20:24, skrev Dirk Eddelbuettel:> > On 1 December 2017 at 19:55, G?ran Brostr?m wrote: > | Hello, > | > | the following is a part of a question asked on R-help. I realized that > | it is better suited for asking here. Apologies for the cross-posting! > | > | I'm on Ubuntu artful, and upgraded with 'apt'. Then > | > | ---------------------------------------------------------------- > | goran at M6800:~/src/R-3.4.3$ /usr/bin/R > | /usr/lib/R/bin/exec/R: symbol lookup error: > | /usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: sgemv_thread_n > | ---------------------------------------------------------------- > | > | Never seen this before. What can I do? > > At home: > > edd at bud:~$ COLUMNS=70 dpkg -l | grep blas > ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i > ii libblas-dev 3.7.0-1 amd64 Basic Linear Algebra Subroutines > ii libblas3 3.7.0-1 amd64 Basic Linear Algebra Reference im > ii libopenblas-ba 0.2.19-2 amd64 Optimized BLAS (linear algebra) l > edd at bud:~$ > > At work: > ........ at .....:~$ COLUMNS=70 dpkg -l | grep blas > ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i > ii libblas-dev 3.7.0-1 amd64 Basic Linear Algebra Subroutines > ii libblas3 3.7.0-1 amd64 Basic Linear Algebra Reference im > ii libcublas8.0:a 8.0.44-3 amd64 NVIDIA cuBLAS Library > ii libnvblas8.0:a 8.0.44-3 amd64 NVBLAS runtime library > ii libopenblas-ba 0.2.19-2 amd64 Optimized BLAS (linear algebra) l > ii libopenblas-de 0.2.19-2 amd64 Optimized BLAS (linear algebra) l > ........ at .....:~$ > > In other words, I tend to use standard blas or openblas or atlas (but > seemingly less often). Both are 17.04, but that doesn't matter as they both > have been updated regularly over the years. > > You must have gotten out of whack between what compiled R, and what runs it. > Did you by chance compile R 3.4.3 locally?Yes, first I installed R-3.4.3 from source and it started OK, but when I tried > library(eha) I got the error above. So I installed by apt, and then I got the above. This is what I always have done, installing both from source and the ubuntu versions via 'apt upgrade', and it has always worked without problems. What has changed now? And how can I get out of this? G?ran> > Dirk >
On 1 December 2017 at 21:12, G?ran Brostr?m wrote: | Yes, first I installed R-3.4.3 from source and it started OK, but when I | tried | | > library(eha) | | I got the error above. At that point I suggest to reinstall eha, and/or do 'ldd' on its shared library to find out what it thinks it is pointing to. The 'threaded gemv' must be coming from somewhere. | So I installed by apt, and then I got the above. You may now have several R's on your system so you need to check your path. Remember /usr/local generally wins so even if you have a self-compiled R and a packaged on 'R' will probably get you /usr/local/bin/R. | This is what I always have done, installing both from source and the | ubuntu versions via 'apt upgrade', and it has always worked without | problems. What has changed now? And how can I get out of this? We cannot tell. This is somewhat incomplete information. It appears to be related to your computer. You may be tired of me saying 'Docker' but it gives you a clean room, akin to installing on a fresh empty machine. Useful for debugging. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk, thanks for your help. At work I have (ubuntu 16.04): ii libblas-common 3.6.0-2ubuntu2 amd64 Dependency package for all BLAS implementations ii libblas-dev 3.6.0-2ubuntu2 amd64 Basic Linear Algebra Subroutines 3, static library ii libblas3 3.6.0-2ubuntu2 amd64 Basic Linear Algebra Reference implementations, shared library and everything works before and after upgrading (/usr/bin/R). However, at home (ubuntu 17.10): goran at M6800:~$ dpkg -l | grep blas ii libblas-dev:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra Subroutines 3, static library ii libblas3:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra Reference implementations, shared library ii libopenblas-base:amd64 0.2.20+ds-4 amd64 Optimized BLAS (linear algebra) library (shared library) and it worked before upgrade but not after. Seems to be missing 'libblas-common'. So I try to install: goran at M6800:~$ sudo apt install libblas-common [sudo] password for goran: Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libblas-common So there is no such package in 17.10, but I have it in 16.04. What can be the replacement? Maybe I should downgrade to R-3.4.2, which works, but it doesn't feel right. G?ran On 2017-12-01 21:12, G?ran Brostr?m wrote:> > > Den 2017-12-01 kl. 20:24, skrev Dirk Eddelbuettel: >> >> On 1 December 2017 at 19:55, G?ran Brostr?m wrote: | Hello, | | the >> following is a part of a question asked on R-help. I realized that >> | it is better suited for asking here. Apologies for the >> cross-posting! | | I'm on Ubuntu artful, and upgraded with 'apt'. >> Then | | >> ---------------------------------------------------------------- | >> goran at M6800:~/src/R-3.4.3$ /usr/bin/R | /usr/lib/R/bin/exec/R: >> symbol lookup error: | /usr/lib/x86_64-linux-gnu/libblas.so.3: >> undefined symbol: sgemv_thread_n | >> ---------------------------------------------------------------- | >> | Never seen this before. What can I do? >> >> At home: >> >> edd at bud:~$ COLUMNS=70 dpkg -l | grep blas ii libblas-common >> 3.7.0-1 amd64 Dependency package for all BLAS i ii >> libblas-dev 3.7.0-1 amd64 Basic Linear Algebra >> Subroutines ii libblas3 3.7.0-1 amd64 Basic >> Linear Algebra Reference im ii libopenblas-ba 0.2.19-2 amd64 >> Optimized BLAS (linear algebra) l edd at bud:~$ >> >> At work: ........ at .....:~$ COLUMNS=70 dpkg -l | grep blas ii >> libblas-common 3.7.0-1 amd64 Dependency package for all >> BLAS i ii libblas-dev 3.7.0-1 amd64 Basic Linear >> Algebra Subroutines ii libblas3 3.7.0-1 amd64 >> Basic Linear Algebra Reference im ii libcublas8.0:a 8.0.44-3 >> amd64 NVIDIA cuBLAS Library ii libnvblas8.0:a 8.0.44-3 >> amd64 NVBLAS runtime library ii libopenblas-ba 0.2.19-2 >> amd64 Optimized BLAS (linear algebra) l ii libopenblas-de >> 0.2.19-2 amd64 Optimized BLAS (linear algebra) l >> ........ at .....:~$ >> >> In other words, I tend to use standard blas or openblas or atlas >> (but seemingly less often). Both are 17.04, but that doesn't >> matter as they both have been updated regularly over the years. >> >> You must have gotten out of whack between what compiled R, and what >> runs it. Did you by chance compile R 3.4.3 locally? > > Yes, first I installed R-3.4.3 from source and it started OK, but > when I tried > >> library(eha) > > I got the error above. > > So I installed by apt, and then I got the above. > > This is what I always have done, installing both from source and the > ubuntu versions via 'apt upgrade', and it has always worked without > problems. What has changed now? And how can I get out of this? > > G?ran >> >> Dirk >> > > _______________________________________________ R-SIG-Debian mailing > list R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Hi there, On 1 December 2017 at 23:24, G?ran Brostr?m wrote: | Dirk, | | thanks for your help. At work I have (ubuntu 16.04): | | ii libblas-common 3.6.0-2ubuntu2 amd64 Dependency package for | all BLAS implementations | ii libblas-dev 3.6.0-2ubuntu2 amd64 Basic Linear Algebra | Subroutines 3, static library | ii libblas3 3.6.0-2ubuntu2 amd64 Basic Linear Algebra | Reference implementations, shared library | | and everything works before and after upgrading (/usr/bin/R). However, | at home (ubuntu 17.10): | | goran at M6800:~$ dpkg -l | grep blas | ii libblas-dev:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra | Subroutines 3, static library | ii libblas3:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra | Reference implementations, shared library | ii libopenblas-base:amd64 0.2.20+ds-4 amd64 Optimized BLAS | (linear algebra) library (shared library) | | and it worked before upgrade but not after. Seems to be missing | 'libblas-common'. Maybe. Maybe not. Did you check packages.ubuntu.com (or another source) to see if it still exists? Per https://packages.ubuntu.com/search?keywords=libblas-common it is only listed for xenial (16.04) and zesty (17.04), not your 17.10. | So I try to install: | | goran at M6800:~$ sudo apt install libblas-common | [sudo] password for goran: | Reading package lists... Done | Building dependency tree | Reading state information... Done | E: Unable to locate package libblas-common | | So there is no such package in 17.10, but I have it in 16.04. What can | be the replacement? Maybe I should downgrade to R-3.4.2, which works, | but it doesn't feel right. No that would not be right. To recap: you have an issue on 17.10 only, and the R is self-built or the one installable as binary via CRAN? Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org