[R-sig-Debian] undefined symbol: sgemv_thread_n

[Göran Broström]

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.

Göran

On 2017-12-01 21:12, Göran Broström wrote:
> 
> 
> Den 2017-12-01 kl. 20:24, skrev Dirk Eddelbuettel:
>> 
>> On 1 December 2017 at 19:55, Göran Broström 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?
> 
> Göran
>> 
>> Dirk
>> 
> 
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