Getting mysterious WARNING / Error messages during package installations

question

#1

Dear Sirs,

I just installed Julia for the first time. I’m using an Ubuntu 16.04 machine, and I used Elliot Saba’s PPA.

When I run Pkg.add("…") for any package, I see the following errors:

WARNING: Error during initialization of module LinAlg:
ErrorException("could not load library "liblapack.so.3"
liblapack.so.3.so: cannot open shared object file: No such file or directory")
WARNING: Error during initialization of module CHOLMOD:
ErrorException("could not load library "libcholmod"
/usr/lib/liblapack.so.3: undefined symbol: gotoblas")

I do have libcholomod and liblapack installed. I also had openblas installed before I installed julia.
What can I do to ensure everything works properly and the warnings disappear?


#2

You could try the official binaries instead. They are available from the JuliaLang website.


#3

Ccing @staticfloat for possible fix.


#4

@Greg; what versions of openblas and liblapack do you have installed? You can find via dpkg -l, like this:

$ dpkg -l | grep openblas
ii  libopenblas-base                       0.2.10.1-trusty2                              amd64        Optimized BLAS (linear algebra) library based on GotoBLAS2
ii  libopenblas-dev                        0.2.10.1-trusty2                              amd64        Optimized BLAS (linear algebra) library based on GotoBLAS2
$ dpkg -l | grep lapack
ii  liblapack-dev                          3.5.0-2ubuntu1                                amd64        Library of linear algebra routines 3 - static version
ii  liblapack3                             3.5.0-2ubuntu1                                amd64        Library of linear algebra routines 3 - shared version

If your versions are significantly different, when was the last time you ran sudo apt update && sudo apt upgrade?


#5

@kristoffer.carlsson, @dpsanders, and @staticfloat, thank you for such prompt response! This encourages me to continue trying out Julia :slight_smile:

@kristoffer.carlsson, thanks, I will surely try the official binaries if we can’t resolve this otherwise.

@staticfloat here is the output of my dpkg -l:

algomorph@Juggernaut:~$ dpkg -l | grep openblas
ii  libopenblas-base                                     0.2.18-1ubuntu1                               amd64        Optimized BLAS (linear algebra) library (shared library)
ii  libopenblas-dev                                      0.2.18-1ubuntu1                               amd64        Optimized BLAS (linear algebra) library (development files)
algomorph@Juggernaut:~$ dpkg -l | grep lapack
ii  liblapack-dev                                        3.6.0-2ubuntu2                                amd64        Library of linear algebra routines 3 - static version
ii  liblapack3                                           3.6.0-2ubuntu2                                amd64        Library of linear algebra routines 3 - shared version

#6

Apparently, the PPA I referenced and used to install Julia is the one containing “official binaries”, see http://julialang.org/downloads/platform.html, the Ubuntu section.


#7

In the Linux section, it says “It is strongly recommended that the official generic linux binaries from the downloads page be used to install Julia. The following distribution-specific packages are community contributed.”

Have you tried using the generic linux binaries? This should be easy to try.


#8

Thanks for your response! I have removed the PPA version, downloaded the official archive, and, for lack of any clear instructions, just stuffed the corresponding folders in my /usr/local (bin, share, etc, lib, include) with the corresponding contents from the archive.

The error has gone away. I have filed a bug report with the PPA maintainer.


#9

You can also just make a symbolic link in e.g. /usr/bin/ to the binary that exists at /bin/julia in the compressed archive. That way you don’t have to move around so many files.