* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/PUMP.Rcheck’
* using R Under development (unstable) (2026-07-18 r90269)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-07-18 14:12:52 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘PUMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PUMP’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘PowerUpR’
* 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 ‘PUMP’ can be installed ... 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 ... [12s/13s] OK
* checking Rd files ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [24s/25s]
 [24s/25s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library( testthat )
  > library( PUMP )
  > 
  > test_check("PUMP")
  Saving _problems/test-pump_sample-233.R
  mdes grid result: d2.1_m2fr d_m
  Varying across ICC.2
    nbar: 80	J: 23	Tbar: 0.5
    alpha: 0.05	
    Level:
      1: R2: 0.6 (5 covariates)
      2:   fixed effects  	ICC: ***	omega: 0.4
    rho = 0
    MTP       d_m ICC.2 Adjusted.MDES D1indiv.power
   None d2.1_m2fr 0.200         0.192         0.800
   None d2.1_m2fr 0.400         0.257         0.800
  	0.005 <= MCSE <= 0.005
  	(max.steps = 20  tnum = 1000  start.tnum = 100  final.tnum = 4000  tol = 0.02)
  sample result: d3.2_m3ff2rc d_m with 4 outcomes
  
    target D3indiv power: 0.80
    MDES vector: 0.2, 0.1, 0.05, 2
    nbar: *	J: 3	K: 10	Tbar: 0.5
    alpha: 0.05	
    Level:
      1: R2: 0.4 / 0.9 / 0.1 / 0.5 (5 covariates)
      2: R2: 0.7 (3 covariates)	ICC: 0 / 0.05 / 0.2 / 0.4	omega: 0
      3:   fixed effects  	ICC: 0.4	omega: 0
    rho = 0.4
   MTP Sample.type Sample.size D3indiv.power
    BF        nbar    21.48493           0.8
  	(max.steps = 20  tnum = 200  start.tnum = 20  final.tnum = 800  tol = 0.01)
  mdes result: d3.2_m3ff2rc d_m with 4 outcomes
  
    target min1 power: 0.80
    nbar: 100	J: 3	K: 10	Tbar: 0.5
    alpha: 0.05	
    Level:
      1: R2: 0.4 / 0.9 / 0.1 / 0.5 (5 covariates)
      2: R2: 0.7 (3 covariates)	ICC: 0 / 0.05 / 0.2 / 0.4	omega: 0
      3:   fixed effects  	ICC: 0.4	omega: 0
    rho = 0.4
   MTP Adjusted.MDES min1.power   SE
    BF    0.09130059   0.803125 0.01
  	(7 steps in search)
  	(max.steps = 20  tnum = 400  start.tnum = 40  final.tnum = 1600  tol = 0.02)
  [ FAIL 1 | WARN 0 | SKIP 43 | PASS 224 ]
  
  ══ Skipped tests (43) ══════════════════════════════════════════════════════════
  • On CRAN (42): 'test-cor.R:32:5', 'test-designs_three.R:14:1',
    'test-designs_two.R:13:1', 'test-grid_functions.R:30:3',
    'test-grid_functions.R:141:3', 'test-grid_functions.R:168:3',
    'test-grid_functions.R:197:3', 'test-grid_functions.R:246:3',
    'test-grid_functions.R:269:3', 'test-numZero_parameter.R:5:1',
    'test-plots.R:4:1', 'test-porter-benchmark.R:6:5', 'test-pump_mdes.R:37:3',
    'test-pump_mdes.R:118:3', 'test-pump_mdes.R:151:3', 'test-pump_mdes.R:175:5',
    'test-pump_mdes.R:214:3', 'test-pump_mdes.R:232:3', 'test-pump_mdes.R:252:3',
    'test-pump_mdes.R:323:5', 'test-pump_power.R:38:3', 'test-pump_power.R:96:3',
    'test-pump_power.R:138:3', 'test-pump_power.R:163:3',
    'test-pump_power.R:209:3', 'test-pump_power.R:244:5',
    'test-pump_power.R:264:5', 'test-pump_power.R:284:3',
    'test-pump_power.R:312:5', 'test-pump_power.R:361:3',
    'test-pump_power.R:394:3', 'test-pump_power.R:415:5',
    'test-pump_power.R:452:5', 'test-pump_power.R:552:5',
    'test-pump_power.R:603:5', 'test-pump_power.R:645:5',
    'test-pump_sample.R:423:5', 'test-pump_sample.R:488:5',
    'test-pump_sample.R:561:5', 'test-pumpgridresult.R:37:5',
    'test-update_functions.R:78:5', 'test-update_functions.R:107:5'
  • {PowerUpR} is not installed. (1): 'test-powerup.R:3:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pump_sample.R:233:3'): pump_sample 2 level/2 level ───────────
  Expected `p2[2, "indiv.mean"]` to equal 0.8.
  Differences:
  1/1 mismatches
  [1] 0.821 - 0.8 == 0.021
  
  [ FAIL 1 | WARN 0 | SKIP 43 | PASS 224 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [53s/55s] 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
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/PUMP.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:30.94, 132.79 + 7.28