test oce for R 4.0

[dankelley]

A release candidate is available for R-4.0, and developers have been asked to test their packages against it. I'll do this for oce.

[dankelley]

Below is a diary of my work on this task. (NOTE: this comment will be edited in-place as I go through the steps, so that it will form a self-contained diary, even if the work is done over the course of several sessions.)

Step 1: building

Trial builds told me that some other packages had to be installed first:

1. install.packages("roxygen2")
2. install.packages("testthat")
3. install.packages("gsw")
4. install.packages("rgdal")

At this stage,

R CMD build oce

yields

* checking DESCRIPTION meta-information ...Warning in strsplit(x, "\n[ \t\n]*\n", perl = TRUE) :  PCRE JIT compilation error
	'no more memory'

and then many warnings of that form. Eventually I see

 OK
* cleaning src

and then many more warnings of similar form, e.g.

Warning in sub(re, "", x, perl = TRUE) :
  PCRE JIT compilation error
        'no more memory'

After many screens full of warnings like that, I eventually see

* installing the package to build vignettes

which tells me that things are on-track. This pattern of many warnings followed by a usual build message, continues through the stages of building.

Eventually, I see

Packages suggested but not available:
  'akima', 'automap', 'DBI', 'lubridate', 'ncdf4', 'ocedata', 'raster',
  'rgeos', 'rmarkdown', 'RSQLite', 'R.utils', 'sf', 'tiff', 'XML'
...
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

so I tried that, i.e.

_R_CHECK_FORCE_SUGGESTS_=false R CMD BUILD --compact-vignettes="qpdf" oce

with that, I get tons of the warnings note above, but it eventually completes.

Step 2: checking

_R_CHECK_FORCE_SUGGESTS_=false R CMD CHECK --run-donttest --as-cran oce_1.2-1.tar.gz

Again, I see warnings about PCRE JIT compilation errors, but it eventually completes.

Step 3: installing

R CMD INSTALL oce_1.2-1.tar.gz

produces warnings as above, but completes.

[dankelley]

This is phase 2, with tests with all recommended packages installed.

I installed with

install.packages(c("akima", "automap", "DBI", "lubridate", "ncdf4", "ocedata", "raster", "rgeos", "rmarkdown", "RSQLite", "R.utils", "sf", "tiff", "XML"))

and then did as follows.

Step 1: Build

R CMD BUILD oce

which produced many PCRE JIT warnings as mentioned in the previous comments, but eventually it completed. I looked in

Step 2: Check

When I do

R CMD check oce_1.2-1.tar.gz

I get some progress, but it fails, as follows.

* checking DESCRIPTION meta-information ... ERROR
Warning messages:
1: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
2: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
3: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
4: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
5: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
6: In sub(re, "", x, perl = TRUE) : PCRE JIT compilation error
	'no more memory'
* DONE

I looked in oce.Rcheck/00check.log but I cannot find any more information on why the check yields an ERROR.

[dankelley]

An update to R-4.0/macos was provided after my earlier tests, and those warnings have now vanished. I did have to alter some tests in which I was checking the names of items in objects, and I think this is because now there is a different convention with respect to upper/lower case.

With these changes "develop" commit 2b9506d builds and tests cleanly, both in RStudio and with R CMD. The only hickup is a warning

Compilation used the following non-portable flag(s):
  ‘-mmacosx-version-min=10.13’

[dankelley]

I'v been using R4 for quite a while, so I'm closing this.