-
Notifications
You must be signed in to change notification settings - Fork 96
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
CRAN breaking monitor #647
Comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.pca
,ca
&pco
functions (Suggestion : Add functions for PCA and CA that just callrda()
andcca()
in the background #655) name clash breaks some packages (Addingpca
andca
(wish of #655) breaks two packages in reverse dependencies tests #664)Here test changes against 2.6-6 with comments (last tested with vegan 2.7-0 tagged as
2.6-7-280-ge4770971
on 2024-08-28):adonis
summary.cca
pca, ca & pco
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:It seems that GUniFrac, PCPS, microbiomeExplorer, multiWGCNA and omicplot should be fixed and move from
adonis
toadonis2
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 usevegan::adonis2
. BiodiversityR (foradonis2
), MicrobiotaProcess and QFASA seem to be OK, and the other packages are dealt with those that fail tests.The text was updated successfully, but these errors were encountered: