##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCheck_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iCheck.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCheck’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘iCheck’ 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 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) R2PlotFunc.Rd:74: Lost braces; missing escapes or markup?
    74 |  'las' numeric in {0,1,2,3}; the style of axis labels.
       |                   ^
checkRd: (-1) genSimData.BayesNormal.Rd:93: Lost braces; missing escapes or markup?
    93 | contains 2 columns: \code{arrayID} (array id) and {memSubj} (subject
       |                                                   ^
checkRd: (-1) lmFitWrapper.Rd:85: Lost braces
    85 | code{pval} (p-values of the tests for the covariate of interest, i.e.
       |     ^
checkRd: (-1) plotCurves.Rd:75: Lost braces; missing escapes or markup?
    75 |  'las' numeric in {0,1,2,3}; the style of axis labels.
       |                   ^
checkRd: (-1) plotQCCurves.Rd:102: Lost braces; missing escapes or markup?
   102 |  'las' numeric in {0,1,2,3}; the style of axis labels.
       |                   ^
checkRd: (-1) plotSamplep95p05.Rd:92: Lost braces; missing escapes or markup?
    92 |  'las' numeric in {0,1,2,3}; the style of axis labels.
       |                   ^
checkRd: (-1) quantilePlot.Rd:78: Lost braces; missing escapes or markup?
    78 |  'las' numeric in {0,1,2,3}; the style of axis labels.
       |                   ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/iCheck.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iCheck
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘iCheck’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (iCheck)