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 (last tested with vegan 2.6-7-87-g4a1e8acaf on 2024-06-04):

adonis

• betaper examples ERROR: patch emailed 2024-04-30
• GCalignR re-building of vignette outputs ERROR: PR 2024-05-17
• hagis FIXED on CRAN
• mefa FIXED on CRAN
• microbial FIXED on CRAN
• MMUPHin FIXED (Bioconductor package)
• RVAideMemoire examples ERROR: author contacted 2024-04-24
• SigTree examples & re-building of vignette outputs ERROR: patch emailed 2024-04-30
• smartsnp examples ERROR: patch emailed 2024-04-30, maintainer responded

summary.cca

• BiodiversityR examples ERROR: patch emailed 2024-05-07
• bipartite FIXED on CRAN
• bipartiteD3 FIXED on CRAN
• pctax FIXED on github, not yet on CRAN

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 the reverse dependence test directory 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

It seems that GUniFrac, PCPS, microbiomeExplorer, multiWGCNA and omicplot should be fixed and move from adonis to adonis2 although they do not fail in tests. Superficially it looks like most of these cases are trivial: internal structure is not accessed and all you need to do is to use vegan::adonis2. BiodiversityR (for adonis2), MicrobiotaProcess and QFASA seem to be OK, and the other packages are dealt with those that fail tests.