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Comments to CRAN for submission

Version 0.8-4

This is a minor maintenance release addressing two issues:

  1. earlier versions of permute used testthat::library_if_available(), which is now defunct and removed from testthat, and
  2. an example in permute used a data set from vegan and hence that package needed to be available when checking permute. This example was not conditional upon vegan being available, which caused problems on the OS X Snowleopard instance of CRAN's check/build farm.

Both issues are rectified in the 0.8-4 release.

Test Environments

  • Linux, Fedora 19 & 20 (r-release & r-devel)
  • Linux, Ubuntu 12.04, via Travis-CI (R 3.2.0)
  • win-builder (r-release & r-devel)

R CMD check information

R CMD check produces only the following point of interest if tested against the current CRAN version of vegan. I have included in permute 0.8-4 reference materials for tests against the 2.3-0 version of vegan that Jari Oksanen, maintainer of that package, intends to release to CRAN this week.

* checking differences from ‘permute-Ex.Rout’ to ‘permute-Ex.Rout.save’ ... OK

235c235
< This is vegan 2.2-1
---
> This is vegan 2.3-0

Reverse dependencies

The output from tools::check_packages_in_dir for checks of reverse dependencies is reproduced below

> summary(out)
Check results for packages in dir '/home/gavin/work/git/permute':

Check status summary:
                  NOTE OK
  Source packages    0  1
  Reverse depends    5  7

Check results summary:
permute ... OK
rdepends_bipartite ... NOTE
* checking DESCRIPTION meta-information ... NOTE
rdepends_cwm ... OK
rdepends_expands ... OK
rdepends_indicspecies ... OK
rdepends_NPC ... OK
rdepends_pRF ... OK
rdepends_RAM ... NOTE
* checking dependencies in R code ... NOTE
rdepends_randomizationInference ... OK
rdepends_rich ... NOTE
* checking dependencies in R code ... NOTE
* checking R code for possible problems ... NOTE
rdepends_Storm ... NOTE
* checking DESCRIPTION meta-information ... NOTE
rdepends_VdgRsm ... OK
rdepends_vegan ... NOTE
* checking Rd cross-references ... NOTE

Comments on the NOTEs

  • bipartite:

      * checking DESCRIPTION meta-information ... NOTE
  Malformed Title field: should not end in a period.

    Not an issue related to permute

  • RAM:

       * checking dependencies in R code ... NOTE
  'library' or 'require' calls in package code:
  ‘Heatplus’ ‘gtable’ ‘indicspecies’ ‘mapproj’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

    Not an issue related to permute

  • rich:

       * checking dependencies in R code ... NOTE
  Packages in Depends field not imported from:
   ‘boot’ ‘permute’ ‘vegan’
   These packages need to be imported from (in the NAMESPACE file)
   for when this namespace is loaded but not attached.

   * checking R code for possible problems ... NOTE
   File ‘rich/R/zzz.R’:
    .onLoad calls:
      packageStartupMessage("This is rich ", utils::packageDescription("rich",     field = "Version"), appendLF = TRUE)

  See section ‘Good practice’ in '?.onAttach'.

  c2cv : SRobs: no visible global function definition for ‘specpool’
  rarc : sSRobs: no visible global function definition for ‘specpool’
  rarc: no visible global function definition for ‘boot’
  raref : sSRobs: no visible global function definition for ‘specpool’
  raref: no visible global function definition for ‘boot’
  raref2 : thinning: no visible global function definition for ‘specpool’
  raref2: no visible global function definition for ‘boot’
  rich : SRobs: no visible global function definition for ‘specpool’
  rich : bspfm: no visible global function definition for ‘boot’
  rich : bspfm: no visible global function definition for ‘boot.ci’
  rich : bspf: no visible global function definition for ‘boot’
  rich : bspf: no visible global function definition for ‘boot.ci’

    Not issues related to permute

  • Storm:

      * checking DESCRIPTION meta-information ... NOTE
  Malformed Title field: should not end in a period.

    Not an issue related to permute

  • vegan:

      * checking Rd cross-references ... NOTE
  Packages unavailable to check Rd xrefs: ‘cclust’, ‘smacof’, ‘picante’

    Not an issue related to permute