v2.0 release

[sashahafner]

@fdalby vignette looks good (I think), issue #31 is OK, progress on #22 and #35, so what else do we need to do?

• Finish updating help file abm.Rd

[sashahafner]

Maybe #30 as well?

[fdalby]

@fdalby vignette looks good (I think), issue #31 is OK, progress on #22 and #35, so what else do we need to do?

• Finish updating help file abm.Rd

I updated the help file. You might want to look it through though - might not be consistent in the formatting? The graze pars bit is around line 67, does that make sense?

[sashahafner]

@fdalby make sure to update the version number in the DESCRIPTION file. Are we aiming for v2.0? Seems good to me--it is quite different from original version and not backwards-compatible.

[sashahafner]

We should also build a package and run a check. There must be a simple way to do that in Windows with RStudio. In Linux I use:

R CMD build ABM --compact-vignettes 
R CMD check --as-cran ABM_1.20.12.tar.gz

Seeing some weird warnings about help file sections hmmm.

[sashahafner]

See #39 for help file issues.

[sashahafner]

May just be one remaining problem found by R CMD check. . .: something wrong with an Rd file, not sure where or what, but could just be a missing or extra } or similar. @fdalby could you take a look? I wanted to ask you to fill in some details anyway.

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Paragraph ended before \@Rhref was complete.
<to be read again> 
                   \par 
l.409 

! Extra }, or forgotten \endgroup.
l.412 }

I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: \begin{list} on input line 404 ended by \end{Rdsection}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: \begin{Rdsection} on input line 404 ended by \end{Source}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: \begin{Source} on input line 404 ended by \end{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
* checking PDF version of manual without index ... ERROR
* skipping checking HTML version of manual: no command ‘tidy’ found
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘ABM-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE

[fdalby]

Hmm I found one ")" to much, but did not see any extra "}". I pushed it now, but I am having trouble reinstalling the package now. Does it have to be build again perhaps, I think you have done something with the CRAN stuff which I don't understand much of - could it be related?

[sashahafner]

How do you install it? I use this from within R to install from GitHub:

devtools::install_github('AU-BCE-EE/ABM')

Does RStudio have some way to install it from the local repo directly?

I didn't do anything with the CRAN network (although there is another ABM package on a completely different topic on CRAN now)--I just use the --as-cran option for checking to check for a lot of possible problems (actually maybe it is more cautious than needed).

[fdalby]

I tried both ways, but makes sense it is not working from Cran then :) I think it is some package update I need.Will try tomorrow again.

[sashahafner]

Sounds good. Only thing I see when installing is a question about updating dependencies, which I've been ignoring for some time. Now with dplyr imported the list has grown! Hope to find a workaround later (#21 ).

> devtools::install_github('AU-BCE-EE/ABM')
Downloading GitHub repo AU-BCE-EE/ABM@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                               
 2: CRAN packages only                
 3: None                              
 4: rlang      (1.1.1 -> 1.1.2) [CRAN]
 5: lifecycle  (1.0.3 -> 1.0.4) [CRAN]
 6: withr      (2.5.0 -> 2.5.2) [CRAN]
 7: vctrs      (0.5.1 -> 0.6.5) [CRAN]
 8: utf8       (1.2.2 -> 1.2.4) [CRAN]
 9: fansi      (1.0.3 -> 1.0.5) [CRAN]
10: tidyselect (1.1.2 -> 1.2.0) [CRAN]
11: dplyr      (1.0.9 -> 1.1.4) [CRAN]
12: deSolve    (1.38  -> 1.40 ) [CRAN]

[sashahafner]

May just be one remaining problem found by R CMD check. . .: something wrong with an Rd file, not sure where or what, but could just be a missing or extra } or similar. @fdalby could you take a look? I wanted to ask you to fill in some details anyway.

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.

Got it with 39081a2ca35a47d777f96ce09bcd77b447236d5f