Skip to content

libRblas.so: cannot open shared object file: No such file or directory

8 messages · Ista Zahn, Dirk Eddelbuettel, Steve Gutreuter

Original
Steve Gutreuter
# 
R 3.5.1 is installed under Linux Mint 19 from binaries r-base and 
r-base-dev from ubuntu bionic-cran35.? Mysteriously, packages using 
libRblas cannot be compiled.? I get: libRblas.so: cannot open shared 
object file: No such file or directory.? And indeed, I find no libRblas.so.

Any ideas about how to fix this?

Thanks,

Steve
Dirk Eddelbuettel
#
On 22 September 2018 at 16:08, Steve Gutreuter wrote:
| R 3.5.1 is installed under Linux Mint 19 from binaries r-base and 
| r-base-dev from ubuntu bionic-cran35.? Mysteriously, packages using 
| libRblas cannot be compiled.? I get: libRblas.so: cannot open shared 
| object file: No such file or directory.? And indeed, I find no libRblas.so.
| 
| Any ideas about how to fix this?

What does   sessionInfo()   show?  For me on this computer it is

  R> sessionInfo()
  R version 3.5.1 (2018-07-02)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Ubuntu 18.04.1 LTS

  Matrix products: default
  BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
  LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
  [...]


If Mint follows the setup I use for the Debian package, then you _never have
libRblas.so_ because we use the _external_ BLAS.  This allows you to switch
to Atlas (tuned BLAS), OpenBLAS (multithreaded), Intel MKL (multithreaded and
possibly a little faster than OpenBLAS but much bigger), ...

Dirk
Steve Gutreuter
# 
Thanks Dirk.? That is what I thought, and sessionInfo() returns:

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C
 ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8
 ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8
 ?[7] LC_PAPER=en_US.UTF-8?????? LC_NAME=C
 ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

so R is indeed aware of a blas.? However, packages that require a blas 
fail to build and return

libRblas.so: cannot open shared object file: No such file or directory

Baffled,

Steve
On 09/22/2018 04:55 PM, Dirk Eddelbuettel wrote:
Ista Zahn
#
On Sat, Sep 22, 2018 at 4:08 PM Steve Gutreuter <sgutreuter at gmail.com> wrote:
Can you show use an example? That is, what code did you run exactly,
and what was the error, exactly?

--Ista
Dirk Eddelbuettel
#
On 23 September 2018 at 09:16, Steve Gutreuter wrote:
| Thanks Dirk.? That is what I thought, and sessionInfo() returns:
| 
| Matrix products: default
| BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
| LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
| 
| locale:
|  ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C
|  ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8
|  ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8
|  ?[7] LC_PAPER=en_US.UTF-8?????? LC_NAME=C
|  ?[9] LC_ADDRESS=C?????????????? LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
| 
| so R is indeed aware of a blas.? However, packages that require a blas 
| fail to build and return
| 
| libRblas.so: cannot open shared object file: No such file or directory

That is an _error_ in the (unnamed by you) package as _wrongly assumes_ each
R installation has a libRblas.so.

On Debian/Ubuntu/Mint/... none of the ones using the package do, yet people
install a bazillion packages (eg Michael's PPA alone has a few thousand).

Dirk
Steve Gutreuter
# 
For example,

install.packages("emplik")

is failing with: libRblas.so: cannot open shared object file: No such 
file or directory

As Dirk pointed out, this is likely an error in the emplik package,


Steve
On 09/23/2018 09:57 AM, Ista Zahn wrote:
Dirk Eddelbuettel
#
On 23 September 2018 at 10:09, Steve Gutreuter wrote:
| For example,
| 
| install.packages("emplik")
| 
| is failing with: libRblas.so: cannot open shared object file: No such 
| file or directory
| 
| As Dirk pointed out, this is likely an error in the emplik package,

I made one educated guess. Now we have more information and can update:

- this is a CRAN package so everybody can check its status:
    https://cloud.r-project.org/web/checks/check_results_emplik.html
  turns out it is picture perfect

- this is a CRAN package so everybody can look at its file on the mirror:
    https://github.com/cran/emplik/tree/master/src
  it does not set a link instruction

so we conclude that the error is local to your system.  _Something_ is going
you did not tell us, so I have to guess some more:

- maybe you built another version of R and it sits in your $PATH before the
  packaged version

- maybe you set build environment versions

Ball back in your court.

Dirk
Steve Gutreuter
# 
Problem solved, but don't know how.? The only error or warning from 
install.packages("emplik") was about libRblas.? However, some other 
packages failed to update for lack of other R packages. Once I fixed 
those other R dependencies, all of the messages about the absence of 
libRblas.so also vanished.

Many thanks for your patience and help.

Steve
On 09/23/2018 10:31 AM, Dirk Eddelbuettel wrote: