- using R Under development (unstable) (2024-04-29 r86495)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-23) 13.2.0
GNU Fortran (Debian 13.2.0-23) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘popEpi/DESCRIPTION’ ... OK
- this is package ‘popEpi’ version ‘0.4.11’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘popEpi’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the package can be unloaded cleanly ... [3s/4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/6s] OK
- checking loading without being on the library search path ... [3s/3s] OK
- checking whether startup messages can be suppressed ... [3s/5s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [38s/59s] OK
- checking Rd files ... [1s/2s] NOTE
checkRd: (-1) survmean.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) survmean.Rd:86-88: Lost braces in \itemize; \value handles \item{}{} directly
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [13s/20s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [71s/109s] ERROR
Running ‘testthat.R’ [71s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
>
> if (requireNamespace("testthat")) {
+ library("testthat")
+ library("popEpi")
+ library("data.table")
+
+ using_r_devel <- grepl(pattern = "devel", x = R.version$status)
+ if (using_r_devel) {
+ ## memory leak problem in data.table 1.11.2 in R-devel (3.6.0 atm)
+ requireNamespace("data.table")
+ data.table::setDTthreads(threads = 1L)
+ }
+
+ testthat::test_check("popEpi")
+ }
Loading required namespace: testthat
NOTE: entry.status has been set to "DM" for all.
first.bad.surv.int last.bad.surv.int surv.obs
<int> <int> <num>
1: 61 120 NaN
first.bad.surv.int last.bad.surv.int surv.obs
<int> <int> <num>
1: 61 120 NaN
Key: <agegr>
agegr first.bad.surv.int last.bad.surv.int surv.obs
<int> <int> <int> <num>
1: 3 61 120 NaN
Key: <agegr>
agegr first.bad.surv.int last.bad.surv.int surv.obs
<int> <int> <int> <num>
1: 3 61 120 NaN
[ FAIL 2 | WARN 0 | SKIP 41 | PASS 269 ]
══ Skipped tests (41) ══════════════════════════════════════════════════════════
• Unit tests skipped normally (41): 'test_aggre.R:162:3', 'test_aggre.R:199:3',
'test_expo.R:4:3', 'test_lexpand.R:5:3', 'test_lexpand.R:29:3',
'test_lexpand.R:59:3', 'test_lexpand.R:78:3', 'test_lexpand.R:99:3',
'test_lexpand.R:137:3', 'test_lexpand.R:213:3', 'test_lexpand.R:249:3',
'test_lexpand.R:342:3', 'test_relpois_mean_curve.R:4:3', 'test_sir.R:221:5',
'test_sir.R:257:3', 'test_splitLexisDT.R:4:3', 'test_splitMulti.R:9:3',
'test_splitting_breaks.R:5:3', 'test_splitting_breaks.R:39:3',
'test_splitting_randomly_on_fixed_data.R:9:3',
'test_splitting_randomly_on_random_data.R:9:3', 'test_survmean.R:6:3',
'test_survmean.R:76:3', 'test_survmean.R:117:3', 'test_survmean.R:166:3',
'test_survmean.R:265:3', 'test_survtab_adjusted.R:4:3',
'test_survtab_observed.R:52:3', 'test_survtab_relative.R:80:5',
'test_survtab_usage.R:6:3', 'test_survtab_usage.R:121:3',
'test_survtab_usage.R:198:3', 'test_survtab_usage.R:432:3',
'test_utils.R:4:3', 'test_utils.R:27:3', 'test_utils.R:138:3',
'test_utils.R:179:3', 'test_weighter.R:5:3', 'test_weighter.R:47:3',
'test_weighter.R:99:3', 'test_weighter.R:122:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_survtab_observed.R:44:3'): surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen ──
cif$V1 not equal to st$CIF_canD.
target is NULL, current is numeric
── Failure ('test_survtab_observed.R:45:3'): surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen ──
cif$V2 not equal to st$CIF_othD.
target is NULL, current is numeric
[ FAIL 2 | WARN 0 | SKIP 41 | PASS 269 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [47s/86s] OK
- checking PDF version of manual ... [8s/17s] OK
- checking HTML version of manual ... [5s/11s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE