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

Mon Dec 20 20:34:49 CET 2021

MatrixExtra 1.9.0 introduced this problem and required something newer
than gcc 8.3.1, e.g. gcc 9.3.1
(https://github.com/david-cortes/MatrixExtra/issues/2).  It's been
fixed in MatrixExtra 0.1.9-1, which is on CRAN since a yesterday or
so.  I've confirmed that this new version installs out of the box on
Ubuntu 18.04 LTS with its default gcc 7.5.0.

/Henrik

On Mon, Dec 20, 2021 at 11:25 AM David Winsemius <dwinsemius using comcast.net> wrote:
>
>
> 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
> >
>
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