Package: PAPi

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAPi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PAPi_1.24.0.tar.gz

StartedAt: 2019-10-16 05:49:23 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:51:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 128.4 seconds

RetCode: 0

Status:  OK

CheckDir: PAPi.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAPi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PAPi_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PAPi.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PAPi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PAPi' version '1.24.0'
* 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 'PAPi' 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
addKeggCodes: no visible global function definition for 'read.csv'
addKeggCodes: no visible global function definition for 'select.list'
addKeggCodes: no visible global function definition for 'write.csv'
buildDatabase : apply_pb: no visible global function definition for
  'txtProgressBar'
buildDatabase : apply_pb : wrapper: no visible global function
  definition for 'setTxtProgressBar'
buildDatabase: no visible global function definition for 'write.csv'
papi: no visible global function definition for 'read.csv'
papi: no visible global function definition for 'select.list'
papi: no visible global function definition for 'txtProgressBar'
papi: no visible global function definition for 'setTxtProgressBar'
papi: no visible global function definition for 'write.csv'
papiHtest : test.t : : no visible global function definition
  for 't.test'
papiHtest : anova.t : : no visible global function
  definition for 'lm'
papiHtest : anova.t: no visible binding for global variable 'anova'
papiHtest: no visible global function definition for 'read.csv'
papiHtest: no visible global function definition for 'p.adjust'
papiHtest: no visible global function definition for 'write.csv'
papiLine: no visible global function definition for 'read.csv'
papiLine: no visible global function definition for 'colors'
papiLine: no visible global function definition for 'png'
papiLine: no visible global function definition for 'par'
papiLine: no visible global function definition for 'plot'
papiLine: no visible global function definition for 'points'
papiLine: no visible global function definition for 'lines'
papiLine: no visible global function definition for 'axis'
papiLine: no visible global function definition for 'text'
papiLine: no visible global function definition for 'legend'
papiLine: no visible global function definition for 'graphics.off'
Undefined global functions or variables:
  anova axis colors graphics.off legend lines lm p.adjust par plot png
  points read.csv select.list setTxtProgressBar t.test text
  txtProgressBar write.csv
Consider adding
  importFrom("grDevices", "colors", "graphics.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "par", "plot",
             "points", "text")
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/PAPi.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PAPi_1.24.0.tar.gz && rm -rf PAPi.buildbin-libdir && mkdir PAPi.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PAPi.buildbin-libdir PAPi_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PAPi_1.24.0.zip && rm PAPi_1.24.0.tar.gz PAPi_1.24.0.zip
###
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install for i386

* installing *source* package 'PAPi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PAPi'
    finding HTML links ... done
    PAPi-package                            html  
    addKeggCodes                            html  
    buildDatabase                           html  
    keggLibrary                             html  
    metabolomicsData                        html  
    papi                                    html  
    papiData                                html  
    papiHtest                               html  
    papiLine                                html  
    papiResults                             html  
** building package indices
** installing vignettes
   'PAPiPackage.Rnw' 
** 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 'PAPi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PAPi' as PAPi_1.24.0.zip
* DONE (PAPi)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PAPi' successfully unpacked and MD5 sums checked