- using R Under development (unstable) (2024-06-26 r86840)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.8 (1)
Debian flang-new version 18.1.8 (1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘metaumbrella/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘metaumbrella’ version ‘1.0.11’
- 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 ‘metaumbrella’ 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 ... [4s/5s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
- checking whether the package can be unloaded cleanly ... [3s/4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
- checking loading without being on the library search path ... [4s/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 ... [48s/53s] OK
- checking Rd files ... [1s/1s] 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 ... [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 ... [45s/58s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
forest.umbrella 8.090 0.054 10.530
subset.umbrella 7.307 0.026 9.295
overlap.prim 6.501 0.128 8.479
forest 4.616 0.076 6.607
drop.evidence 4.176 0.056 5.158
summary.umbrella 4.117 0.083 5.123
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [9m/11m] ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [9m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metaumbrella)
>
> test_check("metaumbrella")
Analyzing factor: A
Analyzing factor: A
Analyzing factor: Pharmacological
Analyzing factor: Pharmacological
Analyzing factor: Pharmacological
Analyzing factor: Physically_active
Analyzing factor: Physically_active
Analyzing factor: Physically_active
The pre/post correlation was calculated using values indicated in studies: Ray (2014) / Livingston (2010) / Israel (2014) / Sosa (2018) / Haulman (2015) / Esquibel (2007) / Ledoux (1982) / Bell (1989) / Canchola (2008) / Gonzalez (2003) / Boucneau (2000)
Analyzing factor: gestational_diabetes
Analyzing factor: gestational_diabetes
Analyzing factor: ASD
Analyzing factor: ASD
Analyzing factor: ASD
Analyzing factor: SSRI
Analyzing factor: SSRI
Analyzing factor: Smoking
Analyzing factor: Smoking
Analyzing factor: Smoking
Analyzing factor: Smoking
Analyzing factor: Gestational_hypertension
Analyzing factor: Gestational_hypertension
Analyzing factor: Pharmacological
Analyzing factor: Pharmacological
Analyzing factor: Surgical
Analyzing factor: ADHD
Analyzing factor: ASD
Analyzing factor: dyslexia
Analyzing factor: ID
Analyzing factor: Yoga
Analyzing factor: Aerobic training
Analyzing factor: Resistance training
Analyzing factor: Mindfulness
Analyzing factor: ID
Analyzing factor: Smoking
Analyzing factor: SSRI
Analyzing factor: Yoga
Analyzing factor: Pharmacological
Analyzing factor: ADHD
Analyzing factor: Pharmacological
Analyzing factor: ADHD
Analyzing factor: A
Analyzing factor: Pharmacological
Analyzing factor: Pharmacological
Analyzing factor: Weisel 2020
In factor 'Weisel 2020':
- study: 'Enock (2014)' contains multiple outcomes
- study: 'Pham (2016)' contains multiple outcomes
In factor 'Weisel 2020' some studies have multiple outcomes but they are not associated with any within-study correlation (which can be indicated in the 'r' column of the dataset). A value of r = 0.5 is assumed.
[ FAIL 1 | WARN 0 | SKIP 59 | PASS 615 ]
══ Skipped tests (59) ══════════════════════════════════════════════════════════
• On CRAN (59): 'test-esb_test.R:10:5', 'test-esb_test.R:77:5',
'test-esb_test.R:138:5', 'test-esb_test.R:181:5', 'test-esb_test.R:234:5',
'test-esb_test.R:247:5', 'test-esb_test.R:299:5', 'test-esb_test.R:354:5',
'test-estimate_n_from_es.R:10:3', 'test-estimate_n_from_es.R:47:3',
'test-estimate_n_from_es.R:94:3', 'test-estimate_n_from_es.R:135:3',
'test-format_dataset.R:12:3', 'test-format_dataset.R:30:3',
'test-format_dataset.R:53:3', 'test-format_dataset.R:75:3',
'test-format_dataset.R:101:3', 'test-format_dataset.R:142:3',
'test-format_dataset.R:176:3', 'test-format_dataset.R:214:3',
'test-format_dataset.R:254:3', 'test-format_dataset.R:305:3',
'test-functions_multilevel.R:5:3', 'test-functions_multilevel.R:51:3',
'test-functions_multilevel.R:86:3', 'test-functions_multilevel.R:119:3',
'test-functions_multilevel.R:164:3', 'test-umbrella.R:8:3',
'test-umbrella.R:15:3', 'test-umbrella.R:47:3', 'test-umbrella.R:61:3',
'test-umbrella.R:82:3', 'test-umbrella.R:96:3', 'test-umbrella.R:124:3',
'test-umbrella.R:153:3', 'test-umbrella.R:172:3', 'test-umbrella.R:191:3',
'test-umbrella.R:415:3', 'test-umbrella.R:428:3', 'test-umbrella.R:446:3',
'test-umbrella.R:461:3', 'test-umbrella.R:477:3', 'test-umbrella.R:491:3',
'test-umbrella.R:510:3', 'test-umbrella.R:529:3', 'test-umbrella.R:547:3',
'test-umbrella.R:572:3', 'test-umbrella.R:589:3', 'test-umbrella.R:604:3',
'test-umbrella.R:624:3', 'test-umbrella.R:641:3', 'test-umbrella.R:658:3',
'test-umbrella.R:675:3', 'test-umbrella.R:692:3', 'test-umbrella.R:709:3',
'test-umbrella.R:726:3', 'test-umbrella.R:746:3', 'test-umbrella.R:791:3',
'test-umbrella.R:836:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_evidence.R:289:3'): df.R ─────────────────────────────────
res2$Class == "I" is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 0 | SKIP 59 | PASS 615 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [161s/205s] OK
- checking PDF version of manual ... [9s/11s] OK
- checking HTML version of manual ... [3s/6s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR