- using R Under development (unstable) (2024-03-25 r86192)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 18.1.2
flang-new version 18.1.2
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘sdmTMB/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘sdmTMB’ version ‘0.4.3’
- 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 ‘sdmTMB’ can be installed ... [6m/20m] OK
See the install log for details.
- used C++ compiler: ‘clang version 18.1.2’
- checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
libs 5.8Mb
- 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 ... [48s/50s] 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [71s/71s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [125s/75s] ERROR
Running ‘testthat.R’ [125s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> options(Matrix.warnDeprecatedCoerce = 2)
>
> library(testthat)
> library(sdmTMB)
>
> test_check("sdmTMB")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ]
══ Skipped tests (146) ═════════════════════════════════════════════════════════
• On CRAN (146): 'test-2-fit-less-basic.R:2:3', 'test-2-fit-less-basic.R:33:3',
'test-2-fit-less-basic.R:86:3', 'test-2-fit-less-basic.R:103:3',
'test-2-fit-less-basic.R:175:3', 'test-2-fit-less-basic.R:194:3',
'test-2-fit-less-basic.R:245:3', 'test-2-fit-less-basic.R:253:3',
'test-2-fit-less-basic.R:283:3', 'test-2-fit-less-basic.R:302:3',
'test-2-fit-less-basic.R:326:3', 'test-2-fit-less-basic.R:371:3',
'test-2-fit-less-basic.R:383:3', 'test-2-fit-less-basic.R:437:3',
'test-2-fit-less-basic.R:512:3', 'test-2-print-anisotropy.R:2:3',
'test-3-families.R:40:3', 'test-3-families.R:61:3', 'test-3-families.R:81:3',
'test-3-families.R:97:3', 'test-3-families.R:133:3',
'test-3-families.R:148:3', 'test-3-families.R:162:3',
'test-3-families.R:180:3', 'test-3-families.R:204:3',
'test-3-spatial-varying.R:2:3', 'test-3-spatial-varying.R:95:3',
'test-3-spatial-varying.R:121:3', 'test-3-spatial-varying.R:142:3',
'test-4-index-calculation.R:4:3', 'test-4-index-calculation.R:60:3',
'test-5-residuals.R:21:3', 'test-5-residuals.R:184:3',
'test-5-residuals.R:285:3', 'test-5-residuals.R:298:3',
'test-5-residuals.R:339:3', 'test-6-tmb-simulation.R:3:3',
'test-6-tmb-simulation.R:36:3', 'test-6-tmb-simulation.R:72:3',
'test-6-tmb-simulation.R:125:3', 'test-7-visreg.R:2:3',
'test-8-delta2.R:2:3', 'test-8-delta2.R:78:3', 'test-8-delta2.R:148:3',
'test-8-delta2.R:255:3', 'test-8-delta2.R:349:3', 'test-8-delta2.R:429:3',
'test-8-delta2.R:479:3', 'test-9-mvn-simulation.R:2:3',
'test-9-mvn-simulation.R:27:3', 'test-9-mvn-simulation.R:53:3',
'test-9-mvn-simulation.R:137:3', 'test-9-mvn-simulation.R:163:3',
'test-9-mvn-simulation.R:237:3', 'test-9-mvn-simulation.R:313:3',
'test-aniso-plots.R:3:3', 'test-cross-validation.R:3:3',
'test-cross-validation.R:53:3', 'test-cross-validation.R:70:3',
'test-cross-validation.R:98:3', 'test-cross-validation.R:236:3',
'test-delta-population-predictions.R:2:3', 'test-delta.R:6:3',
'test-delta.R:53:3', 'test-delta.R:66:3', 'test-delta.R:83:3',
'test-delta.R:97:3', 'test-delta.R:112:3', 'test-delta.R:126:3',
'test-deprecated-args.R:2:3', 'test-deprecated-args.R:67:3',
'test-dharma.R:3:3', 'test-extra-optimization.R:2:3',
'test-extra-time.R:3:3', 'test-extra-time.R:42:3', 'test-extra-time.R:116:3',
'test-factor-levels.R:2:3', 'test-factor-levels.R:37:3',
'test-factor-levels.R:91:3', 'test-forecasting.R:2:3', 'test-index.R:3:3',
'test-link-prediction.R:5:3', 'test-link-prediction.R:67:3',
'test-links.R:2:3', 'test-methods.R:3:3', 'test-methods.R:33:3',
'test-mix.R:3:3', 'test-mix.R:62:3', 'test-mix.R:78:3', 'test-mix.R:97:3',
'test-mix.R:117:3', 'test-nonstationary.R:118:3',
'test-nonstationary.R:164:3', 'test-nonstationary.R:211:3',
'test-nonstationary.R:239:3', 'test-nonstationary.R:290:3',
'test-offset.R:2:3', 'test-offset.R:20:3', 'test-offset.R:81:3',
'test-offset.R:101:3', 'test-parameter-bounds.R:11:3',
'test-prediction-missing-years.R:2:3', 'test-priors.R:23:3',
'test-priors.R:69:3', 'test-priors.R:124:3', 'test-random-intercepts.R:11:3',
'test-random-intercepts.R:125:3', 'test-random-intercepts.R:160:3',
'test-random-intercepts.R:264:3', 'test-reml.R:2:3', 'test-reml.R:74:3',
'test-sanity.R:2:3', 'test-sdmTMB-simulate.R:2:3', 'test-smooths.R:4:3',
'test-smooths.R:16:3', 'test-smooths.R:52:3', 'test-smooths.R:89:3',
'test-smooths.R:127:3', 'test-smooths.R:205:3', 'test-smooths.R:256:3',
'test-smooths.R:279:3', 'test-smooths.R:302:3', 'test-smooths.R:323:3',
'test-smooths.R:345:3', 'test-smooths.R:366:3', 'test-smooths.R:383:3',
'test-smooths.R:400:3', 'test-smooths.R:417:3', 'test-smooths.R:434:3',
'test-smooths.R:445:3', 'test-smooths.R:462:3', 'test-smooths.R:481:3',
'test-threshold-models.R:2:3', 'test-threshold-models.R:18:3',
'test-threshold-models.R:32:3', 'test-time-varying.R:2:3',
'test-time-varying.R:76:3', 'test-tmb-simulation.R:3:3',
'test-tmb-simulation.R:36:3', 'test-tmb-simulation.R:74:3',
'test-tmb-simulation.R:125:3', 'test-utm-conversions.R:2:3',
'test-without-spatial.R:2:3', 'test-1-fit-basic.R:129:3',
'test-1-fit-basic.R:178:3', 'test-1-fit-basic.R:221:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-5-residuals.R:254:3'): Pearson residuals work ────────────────
as.numeric(r) (`actual`) not equal to as.numeric(r1) (`expected`).
actual | expected
[1] 0.14953175 - 0.14953169 [1]
[2] 0.23286508 - 0.23286503 [2]
[3] 0.05429365 - 0.05429360 [3]
[4] 0.48286508 - 0.48286503 [4]
[5] -0.01713492 - -0.01713497 [5]
[6] -0.37427778 - -0.37427783 [6]
[7] -0.01713492 - -0.01713497 [7]
[8] 0.14953175 - 0.14953169 [8]
[9] -0.51713492 - -0.51713497 [9]
[10] 0.08286508 - 0.08286503 [10]
... ... ... and 290 more ...
[ FAIL 1 | WARN 0 | SKIP 146 | PASS 151 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... OK
- checking PDF version of manual ... [10s/11s] 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