deprecate functions that are moved to inbodb

[ElsLommelen]

Deprecation of functions that are moved tot new package inbodb:

• using function gives warning
• asking for documentation refers to list of deprecated functions with replacing functions (but original documentation is still accessible)

[hansvancalster]

@ElsLommelen can you also change the version number to 0.1.0.9081

I don't know a solution to the failed travis checks either. The error is:
ERROR: dependency ‘rmarkdown’ is not available for package ‘pkgdown’ * removing ‘/home/travis/R/Library/pkgdown’

[florisvdh]

The travis error seems to sit here. I.e. htmltools cannot be installed because package ‘Rcpp’ was installed before R 4.0.0: please re-install it.
htmltools > rmarkdown > pkgdown.

Maybe the problem is in htmltools itself; the setup on Travis uses R 3.6.3.

Didn't yet find the actual problem though.

[florisvdh]

But here is a clue.

[florisvdh]

I see no caches for inborutils however; don't know whether they are user-specific though. Maybe @peterdesmet can help here.

Docs on clearing caches are here.

It appears that R 4.0.0 is first installed here, and later R 3.6.3 is installed because it's a dependency of r-cran-rgdal (precompiled ubuntu package). Therein may lie the problem.

[ElsLommelen]

Apparently it is defined in the yaml file, I tried removing it.

[ElsLommelen]

nope, maybe @ThierryO 's suggestions to wait some days till updates to R 4.0.0 are settled in all dependency packages is one of the easiest solutions?
(What I don't understand: 'R package cache' caches packages from the local library, but I am working on a Windows machine. On a Linux machine I often have to install additional features to make packages run (e.g. gdal), where does Travis get these features on my Windows machine?)

[ThierryO]

R 4.0.0 was rolled out just a few days ago. So it hasn't propagated to all repositories. Hence my suggestion to way a couple days or weeks untill it has propagated. This PR doesn't seem to be very urgent.

[florisvdh]

where does Travis get these features on my Windows machine

@ElsLommelen I guess it doesn't because Travis does its work in Linux by default (optionally Mac). In the cloud. The docs for R seem a bit outdated however (currently Ubuntu Xenial is being used).

I guess problem solving will depend on the Travis R build that will have to migrate from current PPA https://launchpad.net/~marutter/+archive/ubuntu/c2d4u3.5 (for downloading r-cran-rgdal and its dependencies, incl R) to a new (yet not existing?) PPA with precompiled packages for R 4.0.0.

[florisvdh]

I got the same problem with n2khab package (errored build).

If you like to fix the travis build (in R 4.0.0), it suffices to drop the binary rgdal package specification from .travis.yml (see inbo/n2khab@3ab00b1), which invokes the installation of precompiled r-cran-rgdal and hence its dependencies from marutter's R 3.5 PPA, overwriting R 4.0.0 with R 3.6.3 (noted above).

The first new build took approx. 40 minutes (compilation of all packages, including rgdal, in R 4.0.0), but I assume that the cache on Travis will make this more efficient in later builds. At least it is clear that many more R packages were actively compiled and installed, compared to earlier succesful builds on R 3.6.2 (example from yesterday). I assume this large bulk compilation will happen just once (per R version), we'll see.

[ElsLommelen]

Thanks @florisvdh !

[florisvdh]

FYI I can add that next n2khab Travis builds are indeed much faster, roughly 5 minutes instead of 40. Only one package needed to be installed because of an update on CRAN, apart from the explicitly specified installations of pkgdown and inborutils.