##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAsense.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RNAsense_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RNAsense.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAsense/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAsense' version '1.19.0'
* 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 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
outputGeneTables 174.48   7.23  181.87
plotSSGS         166.80   6.88  173.69
combineResults   167.75   5.05  172.78
getSwitch         79.09   4.13   83.22
getFC             57.48   1.95   59.44
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/RNAsense.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RNAsense
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)