[R-sig-Debian] libRblas.so: cannot open shared object file: No such file or directory

[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

Post by Dirk Eddelbuettel
| 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

[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

[Ista Zahn]

Post by 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?

Can you show use an example? That is, what code did you run exactly,
and what was the error, exactly?

--Ista

Post by Steve Gutreuter
Thanks,
Steve
_______________________________________________
R-SIG-Debian mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

[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

Post by Ista Zahn

Post by 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?

Can you show use an example? That is, what code did you run exactly,
and what was the error, exactly?
--Ista

Post by Steve Gutreuter
Thanks,
Steve
_______________________________________________
R-SIG-Debian mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

[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

Post by Dirk Eddelbuettel
| 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,
https://cloud.r-project.org/web/checks/check_results_emplik.html
turns out it is picture perfect
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
- 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