[R-sig-Debian] [Solved]... was Cpp Error installing CRAN version of MatrixExtra on Ubuntu 18.04

[David Winsemius]

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
>