* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/survivalMPLdc.Rcheck’
* using R Under development (unstable) (2026-02-11 r89404)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-02-12 03:34:02 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘survivalMPLdc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survivalMPLdc’ version ‘0.1.1’
* 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 ‘survivalMPLdc’ can be installed ... [21s/34s] OK
* 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 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 ... [36s/51s] OK
* checking Rd files ... NOTE
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [50s/73s]
 [50s/74s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(survivalMPLdc)
  > 
  > test_check("survivalMPLdc")
  Saving _problems/test_survivalMPLdc-82.R
  Saving _problems/test_survivalMPLdc-87.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_survivalMPLdc.R:79:1'): Testing the MPL estimated regression coefficients versus the true values ──
  Expected `round(mpl_beta_phi_zp[, 1], 7)` to equal `c(-0.5367184, 0.1258855, 0.221752, 0.1782889)`.
  Differences:
  3/4 mismatches (average diff: 3e-07)
  [1] -0.537 - -0.537 == 5e-07
  [2]  0.126 -  0.126 == 2e-07
  [4]  0.178 -  0.178 == 2e-07
  ── Failure ('test_survivalMPLdc.R:84:1'): Testing the MPL estimated regression coefficients versus the true values ──
  Expected `round(mpl_beta_phi_zp[, 2], 8)` to equal `c(0.16322076, 0.01784505, 0.21279377, 0.02124492)`.
  Differences:
  2/4 mismatches (average diff: 8.4e-07)
  [1] 0.163 - 0.163 == -5.00e-08
  [3] 0.213 - 0.213 ==  1.63e-06
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [21m/29m] 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
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/survivalMPLdc.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 33:56.37, 1443.59 + 20.18