testing documentation for untrained users or automation… missing lib: lubridate, nls2 …

[vv01f]

as a newbe to R I try to plot myself …

result on 2nd try after already iterating installation for lubridate …

********************************************************
Note: As of version 1.0.0, cowplot does not change the                                                                    
  default ggplot2 theme anymore. To recover the previous                                                                  
  behavior, execute:                                                                                                      
  theme_set(theme_cowplot())                                 
********************************************************     

Fehler in library(nls2) : es gibt kein Paket namens ‘nls2’                                                                
Ausführung angehalten                                   

not sure its a big problem anywhere else, but here I got errors due to missing libraries after following the advise in the readme… so I was repeating the install procedure for those as well.

• [ ] are those to be added to the list of dependencies or is that a thing on my distro (debian flavor, installed R via sudo apt install r-base r-base-dev, version I got: "R scripting front-end version 3.6.3 (2020-02-29)") only?
• [ ] the above note on cowplot hints me at there might be sth to do as well, what should be done?
• [ ] also I exited the R console with quit(save="default",status=0,runLast=TRUE) – maybe worth mentioning how that is supposed to be done in the documented example
• [x] after that 3 files are updated, not 2 as mentioned in 4th step of the example (+ residuals_plus7.png)
• [ ] how about moving ping graphics to a separate directory?
• [x] documented filename for source data changed
• [ ] maybe source data for SMS/RKI can be pulled in automatically as well…
• [ ] is checking dependencies explicitly (maybe available.packages or package.dependencies) faster than just running?

and the installation took quite a time… which probably is the reason why the plots are not done by gh actions (saw you still updating manually, thats why I was trying).

[psteinb]

To better compare distros, let's add the output of the following somewhere:

$ R
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 31 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.3

• I just ditched nls2. I just used it for testing.

[vv01f]

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.3