Package: prada

Version: 1.54.0

Command: rm -rf prada.buildbin-libdir prada.Rcheck && mkdir prada.buildbin-libdir prada.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=prada.buildbin-libdir prada_1.54.0.tar.gz >prada.Rcheck\00install.out 2>&1 && cp prada.Rcheck\00install.out prada-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=prada.buildbin-libdir --install="check:prada-install.out" --force-multiarch --no-vignettes --timings prada_1.54.0.tar.gz

StartedAt: 2018-04-12 02:14:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:15:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 74.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: prada.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf prada.buildbin-libdir prada.Rcheck && mkdir prada.buildbin-libdir prada.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=prada.buildbin-libdir prada_1.54.0.tar.gz >prada.Rcheck\00install.out 2>&1 && cp prada.Rcheck\00install.out prada-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=prada.buildbin-libdir --install="check:prada-install.out" --force-multiarch --no-vignettes --timings prada_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'prada/DESCRIPTION' ... OK
* this is package 'prada' version '1.54.0'
* 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 'prada' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQluv1n/R.INSTALL37ac64117ab5/prada/man/cytoSet-class.Rd:88: missing file link 'phenoData-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQluv1n/R.INSTALL37ac64117ab5/prada/man/readCytoSet.Rd:11: missing file link 'dir'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'grid' 'methods' 'RColorBrewer' 'rrcov'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysePlate: no visible binding for global variable 'dat'
gatePoints: no visible binding for global variable 'prev'
killProgress: no visible binding for global variable
  '.tkprogress.canceled'
killProgress: no visible global function definition for 'tkdestroy'
killProgress: no visible binding for global variable
  '.tkprogress.window'
progress: no visible global function definition for 'tktoplevel'
progress: no visible global function definition for 'tclVar'
progress: no visible global function definition for 'tkwm.geometry'
progress: no visible binding for global variable '.tkprogress.window'
progress: no visible global function definition for 'tkwm.title'
progress: no visible global function definition for 'tkconfigure'
progress: no visible global function definition for 'tkframe'
progress: no visible global function definition for 'tkfont.create'
progress: no visible binding for '<<-' assignment to
  '.tkprogress.labelText'
progress: no visible binding for global variable
  '.tkprogress.labelText'
progress: no visible global function definition for 'tclvalue<-'
progress: no visible global function definition for 'tklabel'
progress: no visible global function definition for 'tclvalue'
progress: no visible global function definition for 'tkgrid'
progress: no visible global function definition for 'tclRequire'
progress: no visible global function definition for 'tkwidget'
progress: no visible binding for global variable '.tkprogress.iterator'
progress: no visible binding for global variable
  '.tkprogress.fallbackIterator'
progress: no visible global function definition for 'tkbind'
progress : <anonymous>: no visible binding for '<<-' assignment to
  '.tkprogress.canceled'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.iterator'
updateProgress: no visible binding for global variable
  '.tkprogress.iterator'
updateProgress: no visible global function definition for 'tclvalue<-'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.fallbackIterator'
updateProgress: no visible binding for global variable
  '.tkprogress.fallbackIterator'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.labelText'
updateProgress: no visible binding for global variable
  '.tkprogress.labelText'
updateProgress: no visible global function definition for 'tcl'
Undefined global functions or variables:
  .tkprogress.canceled .tkprogress.fallbackIterator
  .tkprogress.iterator .tkprogress.labelText .tkprogress.window dat
  prev tcl tclRequire tclVar tclvalue tclvalue<- tkbind tkconfigure
  tkdestroy tkfont.create tkframe tkgrid tklabel tktoplevel tkwidget
  tkwm.geometry tkwm.title
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.buildbin-libdir/prada/libs/i386/prada.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'prada' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c inPolygon.c -o inPolygon.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.buildbin-libdir/prada/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'prada'
    finding HTML links ... done
    analysePlate                            html  
    as.all                                  html  
    barploterrbar                           html  
    combineFrames                           html  
    csApply                                 html  
    cytoFrame-class                         html  
    cytoSet-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQluv1n/R.INSTALL37ac64117ab5/prada/man/cytoSet-class.Rd:88: missing file link 'phenoData-class'
    data-cytoFrame                          html  
    data-cytoSet                            html  
    devDims                                 html  
    devRes                                  html  
    fitNorm2                                html  
    gate-class                              html  
    gateSet-class                           html  
    getAlphaNumeric                         html  
    getPradaPar                             html  
    new-internal                            html  
    plotNorm2                               html  
    plotPlate                               html  
    readCytoSet                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpQluv1n/R.INSTALL37ac64117ab5/prada/man/readCytoSet.Rd:11: missing file link 'dir'
    readFCS                                 html  
    readFCSaux                              html  
    removeCensored                          html  
    tcltkProgress                           html  
    threePanelPlot                          html  
    thresholds                              html  
    touchFCS                                html  
    vpLocation                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'prada' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c inPolygon.c -o inPolygon.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/prada.buildbin-libdir/prada/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'prada' as prada_1.54.0.zip
* DONE (prada)
In R CMD INSTALL
In R CMD INSTALL