Clean up build checks

[jakobjassmann]

While the package builds and fully works there are currently some data.table related namespace warnings and a dependency issue related to sf and geojsonio when running devtools::check().

[jakobjassmann]

Fixed all errors and addressed most warnings.

• rgee threw an error during the lsat_get_pixel_centers() tests - this was because geojsonio needs to be loaded during testing, not just installed. I fixed the issue by adding it to the package imports. 141b6fa3cdd03e4cc2a999ed60106027991590e8
• something had changed in the pixel coordinates returned by the GEE for the 'lsat_get_pixel_centers()' tests. I checked the returned coordinates (look good) and updated the validation files. No errors now. c9496ac6f97a73d01f47ca90cd6420b327d67b32
• The new example data files provided during the last update were poorly compressed, I compressed them using tools::resaveRdaFiles(xxx, compress = "xz") 96c3e7ae027adecfbc47978e27456cccb952db84
• I cleaned up some of the namespace warnings that the export and helper functions were responsible for. 509dbb4c23d4f4da83a5f6616dfe2a5889d12158 8867a0c57e511081f7ec6128140f8d49d54cdb25 4506f672a0da212ba70274631fdef9043d6399f3 6941928805e72dab4e62599165b14e57bd0e28b1

It's all pretty tidy now, but 2 warnings and 3 notes remain:

0 errors ✔ | 2 warnings ✖ | 3 notes ✖

Warinings 1) non-standard license - as we chose a non-standard license this can be ignored!

  Non-standard license specification:
    Modified MIT
  Standardizable: FALSE

2) dependency and name check warnings (see below) -> The geojsonio warning is an artifact from the rgee error addressed above. This can be ignored. -> @logan-berner The broom library() call issue should be addressed. It is found in lsat_calibrate_poly.R. You would need to make all broom function calls in that file explicit using broom:: and remove the library() call.

  'library' or 'require' call not declared from: 'broom'
  'library' or 'require' call to 'broom' in package code.
    Please use :: or requireNamespace() instead.
    See section 'Suggested packages' in the 'Writing R Extensions' manual.
  Namespace in Imports field not imported from: 'geojsonio'
    All declared Imports should be used.

Notes

• 2 of the 3 notes relate to timestamps and the package size (22.4 MB) . I think it's okay to ignore them.
• The last note relates to Undefined global functions or variables. This should be addressed to some degree.

Here is the list of undefined global functions / variables:

  Undefined global functions or variables:
    . ..keep.bands BIC LANDSAT_7 N Processing abs.zscore avg blue clear
    cloud.cover date.acquired dif.pcnt dif.pcnt.rank doy evi evi2
    fig.list first.yr first.yr.abs.dif geometric.rmse.model gndvi green
    intercept jrc.water kndvi last.yr last.yr.abs.dif latitude lm
    longitude max.doy median min.doy msi n n.obs n.obs.15days n.obs.fac
    n.obs.focal.win n.obs.gs n.q025 n.q500 n.q975 n.yr.obs
    n.yrs.from.focal na.omit nbr ndii ndmi ndvi ndvsi ndwi nir nirv
    obs.id pcnt pcnt.dif psri pull pval qa.pixel qa.radsat quantile red
    sample.id satellite satvi savi sd si.adjustment si.cor.pcntdif
    si.gs.q90 si.max si.max.cor si.max.obs si.max.pred si.max.uncor
    si.uncor.pcntdif slope snow spl.fit spl.fit.max spl.fit.max.doy
    spl.frac.max sr.b6 sun.elevation swir1 swir2 tidy total.change
    total.change.pcnt trend.cat trend.period variable water wdrvi
    write.table x xcal year.rescale
  Consider adding
    importFrom("stats", "BIC", "lm", "median", "na.omit", "quantile", "sd")
    importFrom("utils", "write.table")

• Most come from non-standard evaluation (especially with data.table) - see here: https://www.r-bloggers.com/2019/08/no-visible-binding-for-global-variable/
• BUT some are function calls that were not made explicit (:: notation).

@logan-berner Here, I'd suggest to address all undefined function calls and consider using one of the solutions suggested in the blog entry for the NSE variables. (I'd vote for Option 1 in terms of effort / return).

[logan-berner]

Thanks @jakobjassmann! I addressed the issues specified above:

• No longer use library(broom) in lsat_calibrate_poly.R, made function calls explicit, and added broom to imported packages
• Cleaned up all importFrom() suggestions by making function calls explicit
• Defined a set of global variables using the script R/global_variables.R

After making these updates, check() now returns only 1 warning (non standard license) and 2 notes (package size and geojsonio NAMESPACES). Looks good! I've updated the package version to LandsatTS 1.1.1.