[Solved]... was Cpp Error installing CRAN version of MatrixExtra on Ubuntu 18.04

On 12/20/21 8:49 AM, Dirk Eddelbuettel wrote:

On 20 December 2021 at 15:48, Sebastian Meyer wrote:
| Am 20.12.21 um 15:19 schrieb Dirk Eddelbuettel:
| >
| > On 19 December 2021 at 18:14, David Winsemius wrote:
| > | I initially attempted installation of pkg:MatrixExtra with
| > | `install.packages on my Ubuntu 18.04 LTS system from within RStudio. It
| > | failed with an error attempting to compile a function named "matmul.cpp"
| > | so I tried running R from a Terminal session. Same error. Finally I
| >
| > Well yes. Same system, same compiler and same R.  Can you remind me what
| >
| >     gcc --version
| >
| > says on Ubuntu 18.04.
|
| gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0

That should be good enough.

I also get gcc version:

gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0

| FWIW, "MatrixExtra" installs without problems for me on "ancient"

I am fairly certain that the (accidental ?) mishap of mixing current R,
i.e. his 4.1.2, with a 3.5.1 library is the issue.

It was just an R user library. I don't have a 3.5.1 library. I'll change
it to something that doesn't bother you.

Before: from Sys.getenv()

R_HOME                         /usr/lib/R
R_INCLUDE_DIR                  /usr/share/R/include
R_LIBS_SITE
/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER /home/david/R/x86_64-pc-linux-gnu-library/3.5.1/

After changing R_LIBS_USER value:

R_HOME                         /usr/lib/R
R_INCLUDE_DIR                  /usr/share/R/include
R_LIBS_SITE
/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER                    /home/david/R/Local_user_lib

 > .libPaths( c( "/home/david/R/Local_user_lib", .libPaths()[2:4]) )
 > install.packages("MatrixExtra")

Installing package into ?/home/david/R/Local_user_lib?
(as ?lib? is unspecified)
also installing the dependencies ?Matrix?, ?RhpcBLASctl?, ?float?

trying URL 'https://cloud.r-project.org/src/contrib/Matrix_1.4-0.tar.gz'
Content type 'application/x-gzip' length 2849865 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL
'https://cloud.r-project.org/src/contrib/RhpcBLASctl_0.21-247.1.tar.gz'
Content type 'application/x-gzip' length 41291 bytes (40 KB)
==================================================
downloaded 40 KB

trying URL 'https://cloud.r-project.org/src/contrib/float_0.2-6.tar.gz'
Content type 'application/x-gzip' length 1373196 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL
'https://cloud.r-project.org/src/contrib/MatrixExtra_0.1.9-1.tar.gz'
Content type 'application/x-gzip' length 218705 bytes (213 KB)
==================================================
downloaded 213 KB

* installing *source* package ?Matrix? ...
** package ?Matrix? successfully unpacked and MD5 sums checked
** using staged installation
** libs

---------------snipped intermediate----------

installing to /home/david/R/Local_user_lib/00LOCK-Matrix/00new/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package ?lattice? was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ?Matrix?
* removing ?/home/david/R/Local_user_lib/Matrix?

-------------snipped----

installing to
/home/david/R/Local_user_lib/00LOCK-MatrixExtra/00new/MatrixExtra/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ?Matrix? 1.2.18 was found, but >= 1.3 is required by
?MatrixExtra?
Execution halted

------------end copy------------

Ran `update.packages()` again and found quite a few not-yet-updated
packages, many of them fairly essential, but NOT in the directory you
were worried about, but rather such as in '/usr/lib/R/site-library' and
'/usr/lib/R/library'

-----fragment of listing of outdated packages----------

lattice :
  Version 0.20-41 installed in /usr/lib/R/library built under R 3.6.3
  Version 0.20-45 available at https://cloud.r-project.org

---------


So now I have a bunch of properly updated packages and MatrixExtra
installs without complaint.


** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (MatrixExtra)

--

Thanks for the impetus to change that annoying, but eventually
misleading, local user library name. I'd been meaning to do that for a
while, and thanks for the advice to recheck version numbers. I'm not
quite sure how I got away with this for so long.


--

David.

It has been so long since I converted from pre-4.0.* that I forgot what the
error message looks like but the arcanae one in David's post may qualify.

| > R version 4.1.2 (2021-11-01)
| > Platform: x86_64-pc-linux-gnu (64-bit)
| > Running under: Ubuntu 18.04.6 LTS
| >
| > Matrix products: default
| > BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
| > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
|
| I see openblas in your sessionInfo(). Could that be a problem?

I do not think. Stable interface, unchanged for decades, hot-swappable.

Dirk