CRAN breaking monitor

[jarioksa]

Next vegan release after 2.6-6 is scheduled to have changes that can break CRAN packages (discussion #645). This issue monitors breakage and the goal is to fix all these before the release. I run occasionally test of reverse dependencies agains CRAN release using tools package and post here the latest tests with comments. These tests are not completely fool-proof, but they are similar as ran by the CRAN team. 231 CRAN and Bioconductor packages depended on the vegan when 2.6-6 was released (but the number is volatile). I cannot build all reverse dependencies for reasons not dependent on vegan – Bioconductor packages are particularly painful.

Currently vegan master has these changes that can break other packages:

• summary.cca disallows extracting scores. Breaks some packages.
• summary.decorana is defunct. No breaks.
• adonis is defunct. Breaks several packages.
• orditkplot: no breaks.

Here test changes against 2.6-6 with comments:

git describe --tags 2.6-7-56-geabf8e38 (tagged at cd83c5f7) updated 2024-05-17

Package: betaper
Check: examples
Old result: OK
New result: ERROR
adonis: patch emailed 2024-04-30

Package: BiodiversityR
Check: examples
Old result: OK
New result: ERROR
summary.cca: patch emailed 2024-05-07

Package: bipartite
Check: examples
Old result: OK
New result: ERROR
summary.cca: FIXED in github, not yet on CRAN

Package: bipartiteD3
Check: re-building of vignette outputs
Old result: OK
New result: ERROR
summary.cca: patch emailed  2024-05-10

Package: GCalignR
Check: re-building of vignette outputs
Old result: OK
New result: ERROR
adonis: not inspected

Package: hagis
adonis: FIXED on CRAN

Package: mefa
Check: tests
Old result: OK
New result: ERROR
adonis: not inspected

Package: microbial
adonis: FIXED on CRAN

Package: MMUPHin
Check: re-building of vignette outputs
Old result: OK
New result: ERROR
adonis: not inspected

Package: pctax
Check: examples
Old result: OK
New result: ERROR
summary.cca: FIXED in github, not yet on CRAN

Package: RVAideMemoire
Check: examples
Old result: OK
New result: ERROR
adonis:  author contacted 2024-04-24

Package: SigTree
Check: examples
Old result: OK
New result: ERROR
adonis: patch emailed 2024-04-30

Package: SigTree
Check: re-building of vignette outputs
Old result: OK
New result: ERROR
adonis: patch emailed 2024-04-30

Package: smartsnp
Check: examples
Old result: OK
New result: ERROR
adonis: patch emailed 2024-04-30, maintainer responded

There may also be cases where the use of defunct functions is not detected, because the code is not tested. From the CRAN point of view these do not bother us, but naturally that code should be fixed as well, because intended functionality fails. However, it is difficult to detect those cases. Scanning for possible cases of adonis found some packages that do not appear in the list above:

$ grep -l "adonis(" rdepends_*/00_pkg_src/*/R/*R | cut -d / -f 3,5
BiodiversityR/nested.npmanova.R
GUniFrac/GUniFrac.R
MicrobiotaProcess/method-binary_offspring.R
MicrobiotaProcess/method-mp_adonis_anosim.R
PCPS/FUN.ADONIS.R
QFASA/All_Rep_Code.R
RVAideMemoire/adonis.II.R
SigTree/adonis.tree.R
betaper/adonis_pertables.R
microbial/Functions.R
microbiomeExplorer/inter_module.R
multiWGCNA/diffModuleExpAnalysis.R
omicplotR/internal.R
smartsnp/smart_mva.R
smartsnp/smart_permanova.R

I know in some cases adonis() calls are never used (they may be commented out), but these packages and functions are worth looking at.