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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAsense.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RNAsense_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RNAsense.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAsense/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAsense' version '1.8.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getFC.Rd':
  'DataFrame'

Missing link or links in documentation object '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
outputGeneTables 188.29   0.19  188.58
combineResults   182.61   1.13  183.80
plotSSGS         182.29   0.05  182.35
getSwitch         80.95   0.14   81.09
getFC             70.63   0.12   70.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotSSGS         179.45   0.05  179.58
outputGeneTables 177.86   0.23  178.25
combineResults   163.61   0.38  164.03
getSwitch         91.34   0.02   91.42
getFC             57.26   0.01   57.31
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RNAsense.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RNAsense_1.8.0.tar.gz && rm -rf RNAsense.buildbin-libdir && mkdir RNAsense.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAsense.buildbin-libdir RNAsense_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RNAsense_1.8.0.zip && rm RNAsense_1.8.0.tar.gz RNAsense_1.8.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  815k  100  815k    0     0   950k      0 --:--:-- --:--:-- --:--:--  951k

install for i386

* installing *source* package 'RNAsense' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAsense'
    finding HTML links ... done
    MZsox                                   html  
    finding level-2 HTML links ... done

    combineResults                          html  
    getFC                                   html  
    getSwitch                               html  
    outputGeneTables                        html  
    plotSSGS                                html  
** 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

install for x64

* installing *source* package 'RNAsense' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAsense' as RNAsense_1.8.0.zip
* DONE (RNAsense)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RNAsense' successfully unpacked and MD5 sums checked