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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings monaLisa_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/monaLisa.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.10.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘monaLisa’ can be installed ... OK
* checking installed package size ... 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) calcBinnedKmerEnr.Rd:137-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:140-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:145-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:155-162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:181-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:185-188: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:108-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:130-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:133-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:138-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:166-169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:170-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:29-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:35-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-checkDfValidity.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-iterativeNormForKmers.Rd:35-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-iterativeNormForKmers.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findMotifHits-methods.Rd:142-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:151-152: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:155-156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:41-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) randLassoStabSel.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:52-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:56-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:67-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:71-73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:88-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotMotifHeatmaps 6.218  0.048   6.279
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/monaLisa.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL monaLisa
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘monaLisa’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (monaLisa)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(monaLisa)

> 
> test_check("monaLisa")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 539 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_Homer.R:134:1'

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 539 ]
> 
> proc.time()
   user  system elapsed 
 67.319   5.155  70.095