`{checked}` doesn't install revdeps if they are dependent on other revdeps

[gowerc]

Apologies if this is a user error but it appears that checked doesn't correctly install dependencies of the revsuggests if they themselves are also revsuggests of the package in question.

For example I am currently trying to check the revsuggests of diffdf which are:

• admiral
• admiraldev
• admiralonco
• admiralophtha
• admiralvaccine
• pharmaverseadam
• random.cdisc.data

Important bit is that admiral is dependent on admiraldev however when running {checked} it doesn't appear to actually install admiraldev for admiral to use (full log):

x <- checked::run(checked::new_check_design(checked::rev_dep_check_tasks_df(".", versions = "release")))
<checked> Checks
[0.1s][install] glue finished (restored)
[0.2s][install] rlang finished (restored)
[0.2s][install] cli finished (restored)
[0.3s][install] lifecycle finished (restored)
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[0.4s][install] fansi finished (restored)
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[0.5s][install] fastmap finished (restored)
[0.5s][install] digest finished (restored)
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[0.6s][install] pkgconfig finished (restored)
[0.7s][install] pillar finished (restored)
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[0.8s][install] withr finished (restored)
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[1.7s][install] evaluate finished (restored)
[1.8s][install] yaml finished (restored)
[1.8s][install] askpass finished (restored)
[1.9s][install] processx finished (restored)
[1.9s][install] later finished (restored)
[1.9s][install] stringr finished (restored)
[2.0s][install] purrr finished (restored)
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[3.3s][install] commonmark finished (restored)
[3.3s][install] httpuv finished (restored)
[3.3s][install] brio finished (restored)
[3.4s][install] textshaping finished (restored)
[3.4s][install] rematch2 finished (restored)
[3.5s][install] diffobj finished (restored)
[3.5s][install] backports finished (restored)
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[3.6s][install] lazyeval finished (restored)
[3.6s][install] remotes finished (restored)
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[4.2s][install] waldo finished (restored)
[4.2s][install] praise finished (restored)
[4.3s][install] diffdf (release) started
[4.3s][install] rex finished (restored)
[4.3s][install] httr finished (restored)
[4.4s][install] xmlparsedata finished (restored)
[4.4s][install] cyclocomp finished (restored)
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[4.8s][install] pkgdown finished (restored)
[4.9s][install] testthat finished (restored)
[4.9s][install] hunspell finished (restored)
[5.0s][install] crosstalk finished (restored)
[5.0s][install] covr finished (restored)
[5.0s][install] lintr finished (restored)
[5.1s][install] devtools finished (restored)
[5.1s][install] spelling finished (restored)
[5.2s][install] DT finished (restored)
[5.2s][install] diffdf finished (restored)
[5.3s][install] checkmate finished (restored)
[5.3s][install] rematch finished (restored)
[5.3s][install] cellranger finished (restored)
[5.4s][install] readxl finished (restored)
[5.4s][install] assertthat finished (restored)
[8.3s][install] diffdf (release) finished (6.4s)
[8.4s][check] admiraldev (v1.0.4) started
[11.6s][check] random.cdisc.data (v1.0.4) started
[48.4s][check] admiraldev (v1.0.4) finished (40.0s)
[48.4s][install] metacore started
[49.8s][install] metacore finished (1.3s)
[49.8s][install] metatools started
[52.7s][check] pharmaverseadam (v1.0.4) started
[52.8s][install] metatools finished (1.3s)
[1.8m][check] random.cdisc.data (v1.0.4) finished with 1 NOTE (1.6m)
[1.8m][install] pharmaversesdtm started
[1.8m][install] pharmaversesdtm finished (1.4s)
[1.8m][install] admiraldev started
[1.8m][install] admiraldev finished (1.4s)
[1.8m][install] reactR started
[1.8m][install] reactR finished (1.5s)
[1.8m][install] reactable started
[1.9m][check] admiral (v1.0.4) started
[1.9m][install] reactable finished (1.3s)
[1.9m][check] admiral (v1.0.4) finished with 1 ERROR (3.6s)
[1.9m][install] admiral started
[2.0m][install] admiral finished (1.4s)
[2.0m][check] admiralophtha (v1.0.4) started
[2.1m][check] admiralophtha (v1.0.4) finished with 1 ERROR (2.6s)
[2.1m][check] admiralvaccine (v1.0.4) started
[2.1m][check] admiralvaccine (v1.0.4) finished with 1 ERROR (2.6s)
[2.1m][install] pharmaverseadam started
[2.2m][check] admiralonco (v1.0.4) started
[2.2m][install] pharmaverseadam finished (1.3s)
[2.2m][check] admiralonco (v1.0.4) finished with 1 ERROR (2.6s)
[3.6m][check] pharmaverseadam (v1.0.4) finished with 1 NOTE (2.8m)
Finished in 3.7m


> x
# Check Task Spec 

admiraldev package R CMD check diff 
notes: OK 
warnings: OK 
errors: OK 

random.cdisc.data package R CMD check diff 
notes: NEW ISSUES [1] 
checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb

warnings: OK 
errors: OK 

pharmaverseadam package R CMD check diff 
notes: NEW ISSUES [1] 
checking package dependencies ... NOTE
Packages suggested but not available for checking: 'metacore', 'metatools'

warnings: OK 
errors: OK 

admiral package R CMD check diff 
notes: OK 
warnings: OK 
errors: NEW ISSUES [1] 
checking package dependencies ... ERROR
Package required but not available: ‘admiraldev’

Packages suggested but not available for checking:
  'pharmaversesdtm', 'reactable'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.


admiralophtha package R CMD check diff 
notes: OK 
warnings: OK 
errors: NEW ISSUES [1] 
checking package dependencies ... ERROR
Packages required but not available: 'admiral', 'admiraldev'

Package suggested but not available for checking: ‘pharmaversesdtm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.


admiralvaccine package R CMD check diff 
notes: OK 
warnings: OK 
errors: NEW ISSUES [1] 
checking package dependencies ... ERROR
Packages required but not available: 'admiral', 'admiraldev'

Packages suggested but not available for checking:
  'pharmaversesdtm', 'metatools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.


admiralonco package R CMD check diff 
notes: OK 
warnings: OK 
errors: NEW ISSUES [1] 
checking package dependencies ... ERROR
Packages required but not available: 'admiral', 'admiraldev'

Packages suggested but not available for checking:
  'pharmaversesdtm', 'pharmaverseadam', 'metatools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

[maksymiuks]

Hi @gowerc

Honestly, I'm having trouble reproducing your issue. Could you please reinstall the checked from GitHub and rerun this code?

If the issue persists, could you please share your sessionInfo and zipped output directory?

Here is what I'm getting for the current release version

> results(x)
# Check Task Spec 

admiraldev package R CMD check diff 
notes: OK 
warnings: OK 
errors: OK 

random.cdisc.data package R CMD check diff 
notes: NEW ISSUES [1] 
checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.4Mb

warnings: OK 
errors: OK 

pharmaverseadam package R CMD check diff 
notes: OK 
warnings: OK 
errors: OK 

admiral package R CMD check diff 
notes: NEW ISSUES [1] 
checking data for non-ASCII characters ... NOTE
  Note: found 12 marked UTF-8 strings

warnings: OK 
errors: OK 

admiralophtha package R CMD check diff 
notes: NEW ISSUES [1] 
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lintr’ ‘pharmaversesdtm’ ‘pkgdown’ ‘testthat’
A package should be listed in only one of these fields.

warnings: OK 
errors: OK 

admiralvaccine package R CMD check diff 
notes: OK 
warnings: OK 
errors: OK 

admiralonco package R CMD check diff 
notes: OK 
warnings: OK 
errors: OK 

[gowerc]

Hmm can't replicate the error exactly anymore, that is when using the github version it seems to all run fine:

                            │ S │ OK  N  W  E │ 
        admiraldev (v1.1.1) │ ✓ │ 43  0  0  0 │ 50.6s 
 random.cdisc.data (v1.1.1) │ ! │ 46  1  0  0 │ 2.0m 
        admiraldev (v1.1.1) │ ✓ │ 43  0  0  0 │ 50.6s 
 random.cdisc.data (v1.1.1) │ ! │ 46  1  0  0 │ 2.0m 
   pharmaverseadam (v1.1.1) │ ✓ │ 43  0  0  0 │ 3.4m 
           admiral (v1.1.1) │ ! │ 46  1  0  0 │ 3.3m 
     admiralophtha (v1.1.1) │ ! │ 46  1  0  0 │ 45.4s 
    admiralvaccine (v1.1.1) │ ✓ │ 47  0  0  0 │ 38.7s 

That being said I did run into an error when I tried to use a custom package directory. That is I had a local .Rprofile of:

options("repos" = list(
    "CRAN" = "https://cloud.r-project.org",
    "NCRAN" = "https://packages.roche.com/Non-Validated/latest"
))
if (!dir.exists(".rpkg")) dir.create(".rpkg")
.libPaths(".rpkg", include.site = FALSE)

When using that I got a bunch errors e.g.

> x <- checked::run(checked::new_check_design(checked::rev_dep_check_tasks_df(".", versions = "release")))
                            │ S │ OK  N  W  E │ 
        admiraldev (v1.1.1) │ ⨯ │ 40  0  1  2 │ 29.4s 
 random.cdisc.data (v1.1.1) │ ⨯ │ 43  1  1  2 │ 39.5s 
   pharmaverseadam (v1.1.1) │ ✓ │ 43  0  0  0 │ 3.0m 
           admiral (v1.1.1) │ ⨯ │ 43  1  1  2 │ 52.2s 
     admiralophtha (v1.1.1) │ ⨯ │ 43  1  1  2 │ 36.1s 
    admiralvaccine (v1.1.1) │ ⨯ │ 44  0  1  2 │ 30.1s 
       admiralonco (v1.1.1) │ ⨯ │ 44  0  1  2 │ 28.5s


> x
admiraldev package R CMD check diff 
notes: OK 
warnings: NEW ISSUES [1] 
checking loading without being on the library search path ... WARNING
Error: package or namespace load failed for ‘admiraldev’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘dplyr’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.

[maksymiuks]

@gowerc Thank you a lot! I'll tackle this issue soon however I'm a little bit short on time this week.

[gowerc]

No worries, theres no rush from me at all as I was already able to test my dependencies and release my package update so when ever suits your schedule :)

[maksymiuks]

Hi @gowerc

I'm sorry, but again, I couldn't reproduce the issue despite trying with different libpaths configurations. However, I enhanced the message of possible problems, so if you could try again, I would appreciate it. Additionally, if you could, please specify the output parameter and email me content in case errors arise. It will help me to find the root cause.