All my revdepchecks on R devel were Ok, even though there were new errors in several packages. I have tracked it down to as.data.frame.rcmdcheck returning an empty data frame in rcmdcheck_comparison.
The problem is with rversion which is an empty list(). I think the expectaion is that it should be NULL not an empty list. This happens on R devel, but not in R stable.
All packages involved are dev version. R devel (unstable) (2022-10-19 r83129).
> oldnew <- dget("old-new.txt")
> str(oldnew$new)
List of 19
$ stdout : chr "* using log directory ‘/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/new/gwasrapidd.Rcheck’\n* us"| __truncated__
$ stderr : chr ""
$ status : int 1
$ duration : num 47.7
$ timeout : logi FALSE
$ rversion : list()
$ platform : chr "x86_64-pc-linux-gnu"
$ errors : chr [1:2] "checking examples ... ERROR\nRunning examples in ‘gwasrapidd-Ex.R’ failed\nThe error most likely occurred in:\n"| __truncated__ "checking tests ...\n Running ‘spelling.R’\n Running ‘testthat.R’\n ERROR\nRunning the tests in ‘tests/testtha"| __truncated__
$ warnings : chr(0)
$ notes : chr(0)
$ description: chr "Package: gwasrapidd\nType: Package\nTitle: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog\nVersion: 0"| __truncated__
$ package : chr "gwasrapidd"
$ version : chr "0.99.13"
$ cran : logi TRUE
$ bioc : logi TRUE
$ checkdir : chr "/home/vspinu/Dropbox/dev/lubridate/revdep/checks/gwasrapidd/new/gwasrapidd.Rcheck"
$ test_fail :List of 1
..$ testthat: chr "> library(testthat)\n> library(gwasrapidd)\n> \n> test_check(\"gwasrapidd\")\n[ FAIL 43 | WARN 2 | SKIP 1 | PAS"| __truncated__
$ test_output:List of 1
..$ spelling: chr "> if(requireNamespace('spelling', quietly=TRUE))\n+ spelling::spell_check_test(vignettes = TRUE, error = FALS"| __truncated__
$ install_out: chr "* installing *source* package ‘gwasrapidd’ ...\n** package ‘gwasrapidd’ successfully unpacked and MD5 sums chec"| __truncated__
- attr(*, "class")= chr "rcmdcheck"
> as.data.frame(oldnew$new, which = "new")
[1] which platform package version type output hash
<0 rows> (or 0-length row.names)
>
> oldnew$new$rversion <- "xx"
> as.data.frame(oldnew$new, which = "new")
which platform rversion package version type
1 new x86_64-pc-linux-gnu xx gwasrapidd 0.99.13 error
2 new x86_64-pc-linux-gnu xx gwasrapidd 0.99.13 error
output
1 checking examples ... ERROR\nRunning examples in ‘gwasrapidd-Ex.R’ failed\nThe error most likely occurred in:\n\n> ### Name: get_variants\n> ### Title: Get GWAS Catalog variants\n> ### Aliases: get_variants\n> \n> ### ** Examples\n> \n> # Get variants by study identifier\n> get_variants(study_id = 'GCST001085', warnings = FALSE)\nError in if (is.numeric(x) && any(x > 1900)) { : \n missing value where TRUE/FALSE needed\nCalls: get_variants ... <Anonymous> -> .parse_xxx_hms -> unlist -> lapply -> FUN\nExecution halted
2 checking tests ...\n Running ‘spelling.R’\n Running ‘testthat.R’\n ERROR\nRunning the tests in ‘tests/testthat.R’ failed.\nLast 13 lines of output:\n } else {\n as.character(x)\n }`: missing value where TRUE/FALSE needed\n Backtrace:\n ▆\n 1. └─gwasrapidd:::empty_to_na(empty_date) at test-utils.R:38:2\n 2. └─lubridate::ymd_hms(NA_real_)\n 3. └─lubridate:::.parse_xxx_hms(...)\n 4. ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)\n 5. └─base::lapply(list(...), .num_to_date)\n 6. └─lubridate (local) FUN(X[[i]], ...)\n \n [ FAIL 43 | WARN 2 | SKIP 1 | PASS 642 ]\n Error: Test failures\n Execution halted
hash
1 ade6d4b9f98a6eb27d5b3726e433fb12
2 81f642311a79a6f2aa2899b9dd6774af
All my revdepchecks on R devel were Ok, even though there were new errors in several packages. I have tracked it down to
as.data.frame.rcmdcheckreturning an empty data frame inrcmdcheck_comparison.The problem is with
rversionwhich is an emptylist(). I think the expectaion is that it should be NULL not an empty list. This happens on R devel, but not in R stable.All packages involved are dev version. R devel
(unstable) (2022-10-19 r83129).old-new.txt