* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/popEpi.Rcheck’
* using R Under development (unstable) (2024-04-24 r86484)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 whether package ‘popEpi’ can be installed ... [30s/36s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/popEpi-00install.html' for details.
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [57s/64s] OK
* checking Rd files ... 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 ... 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 ... [20s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [90s/90s] ERROR
  Running ‘testthat.R’ [89s/90s]
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 ... [72s/72s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE