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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAsense.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAsense_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAsense.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 ‘RNAsense/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAsense’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘RNAsense’ 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 ... NOTE
combineResults: no visible binding for global variable ‘resultSwitch’
combineResults: no visible binding for global variable ‘resultFC’
combineResults : getFCupdown: no visible binding for global variable
  ‘resultFC’
combineResults : getFCupdown: no visible binding for global variable
  ‘name’
combineResults : getFCupdown: no visible binding for global variable
  ‘FCdetect’
getFC: no visible binding for global variable ‘mydata’
getFC: no visible binding for global variable ‘analyzeConditions’
getFC: no visible binding for global variable ‘times’
getSwitch: no visible binding for global variable ‘mydata’
getSwitch: no visible binding for global variable ‘times’
outputGeneTables: no visible binding for global variable
  ‘resultCombined’
outputGeneTables: no visible binding for global variable ‘times’
outputGeneTables: no visible binding for global variable
  ‘analyzeConditions’
outputGeneTables: no visible binding for global variable ‘timepoint’
outputGeneTables: no visible binding for global variable ‘FCdown’
outputGeneTables: no visible binding for global variable ‘FCup’
outputGeneTables: no visible binding for global variable ‘experiment’
plotSSGS: no visible binding for global variable ‘resultCombined’
plotSSGS: no visible binding for global variable ‘times’
plotSSGS: no visible binding for global variable ‘analyzeConditions’
plotSSGS : getFT: no visible binding for global variable ‘result’
plotSSGS : getFT: no visible binding for global variable ‘timepoint’
plotSSGS : getFT: no visible binding for global variable ‘FCdown’
plotSSGS : getFT: no visible binding for global variable ‘FCup’
plotSSGS : <anonymous> : <anonymous> : <anonymous> : <anonymous>: no
  visible binding for global variable ‘experiment’
plotSSGS: no visible binding for global variable ‘xaxis’
plotSSGS: no visible binding for global variable ‘cluster’
Undefined global functions or variables:
  FCdetect FCdown FCup analyzeConditions cluster experiment mydata name
  result resultCombined resultFC resultSwitch timepoint times xaxis
* checking Rd files ... NOTE
checkRd: (-1) MZsox.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MZsox.Rd:13: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'getFC.Rd':
  ‘DataFrame’

Missing link or links in Rd file 'getSwitch.Rd':
  ‘DataFrame’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
combineResults   102.640  3.484 106.500
outputGeneTables  97.372  3.649 101.294
plotSSGS          88.244  3.368  91.709
getSwitch         61.118  1.794  63.106
getFC             21.470  1.781  23.353
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAsense.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAsense
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘RNAsense’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (RNAsense)