non-rpm R libraries not accessible now w R v 4.0.x

[Max Pyziur]

Greetings,

I've installed some R libraries that are not available as rpm packages, 
specifically matlib and a few others.

Recently, R was ported to version 4.0.x and these libraries are not 
callable. When I remove them and try to install them all sorts of 
dependencies are either removed or become problematic.

Any advice?

Much thanks,

Max Pyziur
[e-mail]

[José Abílio Matos]

On Saturday, 18 July 2020 21.22.17 WEST Max Pyziur wrote:
> Greetings,
>
> I've installed some R libraries that are not available as rpm packages,
> specifically matlib and a few others.
>
> Recently, R was ported to version 4.0.x and these libraries are not
> callable. When I remove them and try to install them all sorts of
> dependencies are either removed or become problematic.
>
> Any advice?
>
> Much thanks,
>
> Max Pyziur

What are the errors you are seeing?

All packages need to be rebuilt for R 4.0 be it installed from rpms or 
otherwise. That is a requirement from R 4.0 and not from our installation.

FWIW you can also install packages from cran as rpms using:
https://copr.fedorainfracloud.org/coprs/iucar/cran/

Regards,

[Max Pyziur]

On Sat, 18 Jul 2020, José Abílio Matos wrote:
> On Saturday, 18 July 2020 21.22.17 WEST Max Pyziur wrote:
> > Greetings,
> >
> > I've installed some R libraries that are not available as rpm packages,
> > specifically matlib and a few others.
> >
> > Recently, R was ported to version 4.0.x and these libraries are not
> > callable. When I remove them and try to install them all sorts of
> > dependencies are either removed or become problematic.
> >
> > Any advice?
> >
> > Much thanks,
> >
> > Max Pyziur
>
> What are the errors you are seeing?

As an example:
> install.packages('matlib')

Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
also installing the dependencies ‘crosstalk’, ‘rgl’

trying URL 
'https://packages.othr.de/cran/src/contrib/crosstalk_1.1.0.1.tar.gz'
Content type 'text/plain' length 673125 bytes (657 KB)
==================================================
downloaded 657 KB

trying URL 'https://packages.othr.de/cran/src/contrib/rgl_0.100.54.tar.gz'
Content type 'text/plain' length 2952743 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://packages.othr.de/cran/src/contrib/matlib_0.9.3.tar.gz'
Content type 'text/plain' length 220211 bytes (215 KB)
==================================================
downloaded 215 KB

* installing *source* package ‘crosstalk’ ...
** package ‘crosstalk’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘R6’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘crosstalk’
* removing ‘/usr/lib64/R/library/crosstalk’
ERROR: dependency ‘crosstalk’ is not available for package ‘rgl’
* removing ‘/usr/lib64/R/library/rgl’
ERROR: dependency ‘rgl’ is not available for package ‘matlib’
* removing ‘/usr/lib64/R/library/matlib’

The downloaded source packages are in
    ‘/tmp/Rtmpnvhegn/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("matlib") :
   installation of package ‘crosstalk’ had non-zero exit status
2: In install.packages("matlib") :
   installation of package ‘rgl’ had non-zero exit status
3: In install.packages("matlib") :
   installation of package ‘matlib’ had non-zero exit status

R6 is available as a F32 RPM; however, it comes back w the above error 
message, fyi.
> All packages need to be rebuilt for R 4.0 be it installed from rpms or otherwise. That is a requirement from R 4.0 and not from our installation.
> FWIW you can also install packages from cran as rpms using:
>
> https://copr.fedorainfracloud.org/coprs/iucar/cran/

Thanks; I'll check this out.

Max
> Regards,
>
> --
>
> José Matos

[Max Pyziur]

On Sat, 18 Jul 2020, José Abílio Matos wrote:

[deleted for the sake of brevity ]
> All packages need to be rebuilt for R 4.0 be it installed from rpms or otherwise. That is a requirement from R 4.0 and not from our installation.
>
> FWIW you can also install packages from cran as rpms using:
>
> https://copr.fedorainfracloud.org/coprs/iucar/cran/

I got this far: when doing
dnf install R-CRAN-matlib

the command comes back with a boatload of dependencies, including the 
request to install R-CRAN-R6.

R-R6 as an F32 rpm is already installed; there are other instances where 
an RPM-CRAN-* rpm is requested to be installed as a dependency when the 
comprable F32 rpm is already installed.

This doesn't seem to be prudent.

Max
> Regards,
>
> --
>
> José Matos

[José Abílio Matos]

On Saturday, 18 July 2020 23.46.07 WEST Max Pyziur wrote:
> R6 is available as a F32 RPM; however, it comes back w the above error
> message, fyi.

Are you sure? :-)

What does the following code returns?

ip <- installed.packages()
ip["R6", c(2,3,16)]

[José Abílio Matos]

On Saturday, 18 July 2020 23.58.04 WEST Max Pyziur wrote:
> I got this far: when doing
> dnf install R-CRAN-matlib
>
> the command comes back with a boatload of dependencies, including the
> request to install R-CRAN-R6.
>
> R-R6 as an F32 rpm is already installed; there are other instances where
> an RPM-CRAN-* rpm is requested to be installed as a dependency when the
> comprable F32 rpm is already installed.
>
> This doesn't seem to be prudent.
>
> Max

The packages are, by design, parallel installable with Fedora's packages.

FWIW there is a mailing list specialized in the relation between R and Fedora:
https://stat.ethz.ch/mailman/listinfo/r-sig-fedora

Most of the Fedora R packagers are there, including Iñaki who created the rpm 
cran repository, so it is a nice place to ask these questions.

BTW what are the results when you run

dnf list R-R6

Regards,

[Max Pyziur]

Consolidating our correspondance and answering your two questions ...

On Sun, 19 Jul 2020, José Abílio Matos wrote:
> On Saturday, 18 July 2020 23.46.07 WEST Max Pyziur wrote:
> > R6 is available as a F32 RPM; however, it comes back w the above error
> > message, fyi.
>
> Are you sure? :-)
>
> What does the following code returns?
>
> ip <- installed.packages()
> ip["R6", c(2,3,16)]

ip <- installed.packages()
ip["R6", c(2,3,16)]
> ip <- installed.packages()
> ip["R6", c(2,3,16)]

LibPath                Version                  Built
"/usr/lib64/R/library"                "2.4.1"                "3.6.2"

And separately you asked for the dnf info output

pyz@pegasus ~> dnf info R-r6

Installed Packages
Name         : R-R6
Version      : 2.4.1
Release      : 4.fc32
Architecture : noarch
Size         : 80 k
Source       : R-R6-2.4.1-4.fc32.src.rpm
Repository   : @System
From repo    : updates
Summary      : Classes with Reference Semantics
URL          : http://cran.r-project.org/web/packages/R6/index.html
License      : MIT
Description  : The R6 package allows the creation of classes with 
reference semantics,
              : similar to R's built-in reference classes. Compared to 
reference classes,
              : R6 classes are simpler and lighter-weight, and they are not 
built on S4
              : classes so they do not require the methods package. These 
classes allow
              : public and private members, and they support inheritance, 
even when the
              : classes are defined in different packages.

fyi,

M

[José Abílio Matos]

On Sunday, 19 July 2020 13.15.06 WEST Max Pyziur wrote:
> ip <- installed.packages()
> ip["R6", c(2,3,16)]
> > ip <- installed.packages()
> > ip["R6", c(2,3,16)]
>             LibPath                Version                  Built
>
> "/usr/lib64/R/library"                "2.4.1"                "3.6.2"

That makes (some) sense.

I get this:
> ip["R6", c(2,3,16)]

LibPath                Version                  Built 
"/usr/share/R/library"                "2.4.1"                "4.0.2"

Note that the difference comes from the package location.

I can probably see this from running:

.libPaths()

So that probably means that you have two packages installed, one in /usr/
lib64/R/library and another in /usr/share/R/library. You will see from running 
the command above that /usr/lib64/R/library comes first and so that is the 
package used.

I hope that this makes sense.

Regards,