Error installing and updating R packages

[martinprad0]

I cannot install nor update any package in R and get the following error > install.packages("Rcpp")

Available system packages...

Install system packages...
[SKIPPED] R-littler-0.3.18-4.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64.rpm: Already downloaded 
Error in install.packages : dbus: Call failed: Transaction test error:  package R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64 does not verify: Header V4 RSA/SHA256 Signature, key ID 1a3b4456: NOTTRUSTED

I'm currently using Fedora 38 and this version of the repository: Version : 0.5.5 Release : 1.fc38.copr6331124

Every R related was installed through dnf install. But I cannot identify the problem.

[eddelbuettel]

We actually have a f38 docker container for bspm to with this Dockerfile. Maybe you can eyeball and see any differences? From the top down, bspm really prefers to be installed as root but I am sure you already saw that.

[martinprad0]

Is the command dnf remove R-CoprManager enough to remove any instance of the package? Also, since I'm not very familiar with Docker, I wanted to ask you if I just have to run the Dockerfile with docker and it will install automatically

[eddelbuettel]

Oh, no worries, it basically just provides an "existence proof" that a) yes bspm still works and b) also under f38. In short we would need to know more from you about what you did -- the above does not reveal much, You did catch that it told you it already had Rcpp, right?

Anyway here is quick demo of RcppArmadillo (also fetching Rcpp) in the context of Docker (as my native system is not Fedora):

edd@rob:~$ docker run --rm -ti rocker/r-bspm:f38 Rscript -e 'install.packages("RcppArmadillo")'
Available system packages as root...
Copr repo for cran owned by iucar                                       30 MB/s |  25 MB     00:00    
Fedora 38 - x86_64                                                      23 MB/s |  83 MB     00:03    
Fedora 38 openh264 (From Cisco) - x86_64                               1.4 kB/s | 2.5 kB     00:01    
Fedora Modular 38 - x86_64                                             5.1 MB/s | 2.8 MB     00:00    
Fedora 38 - x86_64 - Updates                                            14 MB/s |  30 MB     00:02 
Install system packages as root...
(1/14): R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64.rpm                12 MB/s | 2.0 MB     00:00    
(2/14): libgomp-13.2.1-1.fc38.x86_64.rpm                               1.5 MB/s | 319 kB     00:00    
(3/14): libgfortran-13.2.1-1.fc38.x86_64.rpm                           3.0 MB/s | 904 kB     00:00    
(4/14): gcc-plugin-annobin-13.2.1-1.fc38.x86_64.rpm                    337 kB/s |  46 kB     00:00    
(5/14): libstdc++-13.2.1-1.fc38.x86_64.rpm                              14 MB/s | 863 kB     00:00    
(6/14): libstdc++-devel-13.2.1-1.fc38.x86_64.rpm                        16 MB/s | 2.6 MB     00:00    
(7/14): R-CRAN-RcppArmadillo-0.12.6.1.0-1.fc38.copr6264944.x86_64.rpm   11 MB/s | 928 kB     00:00    
(8/14): gcc-13.2.1-1.fc38.x86_64.rpm                                    31 MB/s |  34 MB     00:01    
(9/14): gcc-gfortran-13.2.1-1.fc38.x86_64.rpm                           15 MB/s |  12 MB     00:00    
(10/14): libquadmath-13.2.1-1.fc38.x86_64.rpm                          1.2 MB/s | 194 kB     00:00    
(11/14): libquadmath-devel-13.2.1-1.fc38.x86_64.rpm                    833 kB/s |  36 kB     00:00    
(12/14): libgcc-13.2.1-1.fc38.x86_64.rpm                               2.5 MB/s | 109 kB     00:00    
(13/14): cpp-13.2.1-1.fc38.x86_64.rpm                                   19 MB/s |  11 MB     00:00    
(14/14): gcc-c++-13.2.1-1.fc38.x86_64.rpm                              4.6 MB/s |  13 MB     00:02    
  Preparing        :                                                                               1/1 
  Upgrading        : libgcc-13.2.1-1.fc38.x86_64                                                  1/26 
  Running scriptlet: libgcc-13.2.1-1.fc38.x86_64                                                  1/26 
  Upgrading        : libstdc++-13.2.1-1.fc38.x86_64                                               2/26 
  Upgrading        : libquadmath-13.2.1-1.fc38.x86_64                                             3/26 
  Upgrading        : libgomp-13.2.1-1.fc38.x86_64                                                 4/26 
  Installing       : R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64                                 5/26 
  Upgrading        : libstdc++-devel-13.2.1-1.fc38.x86_64                                         6/26 
  Upgrading        : libgfortran-13.2.1-1.fc38.x86_64                                             7/26 
  Upgrading        : cpp-13.2.1-1.fc38.x86_64                                                     8/26 
  Upgrading        : gcc-13.2.1-1.fc38.x86_64                                                     9/26 
  Running scriptlet: gcc-13.2.1-1.fc38.x86_64                                                     9/26 
  Upgrading        : libquadmath-devel-13.2.1-1.fc38.x86_64                                      10/26 
  Upgrading        : gcc-gfortran-13.2.1-1.fc38.x86_64                                           11/26 
  Upgrading        : gcc-c++-13.2.1-1.fc38.x86_64                                                12/26 
  Upgrading        : gcc-plugin-annobin-13.2.1-1.fc38.x86_64                                     13/26 
  Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc38.x86_64                                     13/26 
  Installing       : R-CRAN-RcppArmadillo-0.12.6.1.0-1.fc38.copr6264944.x86_64                   14/26 
  Cleanup          : gcc-gfortran-13.0.1-0.12.fc38.x86_64                                        15/26 
  Cleanup          : libgfortran-13.0.1-0.12.fc38.x86_64                                         16/26 
  Cleanup          : gcc-c++-13.0.1-0.12.fc38.x86_64                                             17/26 
  Cleanup          : gcc-plugin-annobin-13.0.1-0.12.fc38.x86_64                                  18/26 
  Cleanup          : libquadmath-devel-13.0.1-0.12.fc38.x86_64                                   19/26 
  Cleanup          : libstdc++-devel-13.0.1-0.12.fc38.x86_64                                     20/26 
  Cleanup          : libstdc++-13.0.1-0.12.fc38.x86_64                                           21/26 
  Cleanup          : gcc-13.0.1-0.12.fc38.x86_64                                                 22/26 
  Cleanup          : libquadmath-13.0.1-0.12.fc38.x86_64                                         23/26 
  Cleanup          : libgcc-13.0.1-0.12.fc38.x86_64                                              24/26 
  Running scriptlet: libgcc-13.0.1-0.12.fc38.x86_64                                              24/26 
  Cleanup          : cpp-13.0.1-0.12.fc38.x86_64                                                 25/26 
  Cleanup          : libgomp-13.0.1-0.12.fc38.x86_64                                             26/26 
  Running scriptlet: libgomp-13.0.1-0.12.fc38.x86_64                                             26/26 
  Verifying        : R-CRAN-Rcpp-1.0.11-1.fc38.copr6148288.x86_64                                 1/26 
  Verifying        : R-CRAN-RcppArmadillo-0.12.6.1.0-1.fc38.copr6264944.x86_64                    2/26 
  Verifying        : cpp-13.2.1-1.fc38.x86_64                                                     3/26 
  Verifying        : cpp-13.0.1-0.12.fc38.x86_64                                                  4/26 
  Verifying        : gcc-13.2.1-1.fc38.x86_64                                                     5/26 
  Verifying        : gcc-13.0.1-0.12.fc38.x86_64                                                  6/26 
  Verifying        : gcc-c++-13.2.1-1.fc38.x86_64                                                 7/26 
  Verifying        : gcc-c++-13.0.1-0.12.fc38.x86_64                                              8/26 
  Verifying        : gcc-gfortran-13.2.1-1.fc38.x86_64                                            9/26 
  Verifying        : gcc-gfortran-13.0.1-0.12.fc38.x86_64                                        10/26 
  Verifying        : gcc-plugin-annobin-13.2.1-1.fc38.x86_64                                     11/26 
  Verifying        : gcc-plugin-annobin-13.0.1-0.12.fc38.x86_64                                  12/26 
  Verifying        : libgcc-13.2.1-1.fc38.x86_64                                                 13/26 
  Verifying        : libgcc-13.0.1-0.12.fc38.x86_64                                              14/26 
  Verifying        : libgfortran-13.2.1-1.fc38.x86_64                                            15/26 
  Verifying        : libgfortran-13.0.1-0.12.fc38.x86_64                                         16/26 
  Verifying        : libgomp-13.2.1-1.fc38.x86_64                                                17/26 
  Verifying        : libgomp-13.0.1-0.12.fc38.x86_64                                             18/26 
  Verifying        : libquadmath-13.2.1-1.fc38.x86_64                                            19/26 
  Verifying        : libquadmath-13.0.1-0.12.fc38.x86_64                                         20/26 
  Verifying        : libquadmath-devel-13.2.1-1.fc38.x86_64                                      21/26 
  Verifying        : libquadmath-devel-13.0.1-0.12.fc38.x86_64                                   22/26 
  Verifying        : libstdc++-13.2.1-1.fc38.x86_64                                              23/26 
  Verifying        : libstdc++-13.0.1-0.12.fc38.x86_64                                           24/26 
  Verifying        : libstdc++-devel-13.2.1-1.fc38.x86_64                                        25/26 
  Verifying        : libstdc++-devel-13.0.1-0.12.fc38.x86_64                                     26/26 
edd@rob:~$ 

[Enchufa2]

@martinprad0 Sorry for the trouble, but we have an issue with the GPG key on Copr. See #41, and this comment for a workaround while the RPM people solve this issue.

(Note: the existing docker images still work because they have the old key, which is still valid; so refer to the workaround above)

[martinprad0]

Yes! I tried the workaround changing the GPG key and now everything works. You don't know how frustating it was LMAO. But, now everything seems like rainbows and flowers.

[eddelbuettel]

Aren't premade binaries the best (especially when properly integrated with the system as cran2copr and r2u do) ?