R error with plot_avgsizes process

[hkaspersen]

I get the following error message when running the 02_simple_run.nf track, when it comes to the plot_avgsizes process. However, the plot_coverage process works fine, so it seems to be a specific R related issue perhaps?

Command output:
  reshape ggplot2
    FALSE   FALSE

Command error:
  Warning: unable to access index for repository https://cran.uib.no/src/contrib:
    cannot open URL 'https://cran.uib.no/src/contrib/PACKAGES'
  Loading required package: reshape
  Loading required package: ggplot2
  Warning messages:
  1: packages ‘reshape’, ‘ggplot2’ are not available (for R version 3.6.1)
  2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘reshape’
  3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘ggplot2’
  Error in melt(avg_data, id = c("samples")) :
    could not find function "melt"
  Execution halted

From the .command.log file:

Warning: unable to access index for repository https://cran.uib.no/src/contrib:
  cannot open URL 'https://cran.uib.no/src/contrib/PACKAGES'
Loading required package: reshape
Loading required package: ggplot2
reshape ggplot2
  FALSE   FALSE
Warning messages:
1: packages ‘reshape’, ‘ggplot2’ are not available (for R version 3.6.1)
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘reshape’
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Error in melt(avg_data, id = c("samples")) :
  could not find function "melt"
Execution halted

[Thomieh73]

Hi Håkon,
So from the error message it seems it does not want to install the R-packages which is odd. And it is running R version 3.6.1, which is old as well.... Hmmm I have to check what is happening here.