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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genefilter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings genefilter_1.76.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/genefilter.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 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.76.0'
* 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 'genefilter' can be installed ... WARNING
Found the following significant warnings:
  pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/genefilter.Rcheck/00install.out' for details.
* 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 ... NOTE
'library' or 'require' call to 'tkWidgets' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'tkWidgets:::formatArg'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eSetFilter : buildGUI: no visible binding for '<<-' assignment to 'END'
eSetFilter : buildGUI : setFilter: no visible global function
  definition for 'tkget'
eSetFilter : buildGUI : setFilter: no visible global function
  definition for 'tkcurselection'
eSetFilter : buildGUI : setFilter: no visible global function
  definition for 'writeList'
eSetFilter : buildGUI : setFilter: no visible global function
  definition for 'tkconfigure'
eSetFilter : buildGUI : cancel: no visible global function definition
  for 'tkdestroy'
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
  to 'END'
eSetFilter : buildGUI : finish: no visible global function definition
  for 'tkdestroy'
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for 'tkget'
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for 'tkcurselection'
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for 'tkconfigure'
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for 'writeText'
eSetFilter : buildGUI : pickedSel: no visible global function
  definition for 'tkconfigure'
eSetFilter : buildGUI : remove: no visible global function definition
  for 'tkget'
eSetFilter : buildGUI : remove: no visible global function definition
  for 'tkcurselection'
eSetFilter : buildGUI : remove: no visible global function definition
  for 'writeList'
eSetFilter : buildGUI : remove: no visible global function definition
  for 'tkconfigure'
eSetFilter : buildGUI: no visible global function definition for
  'tktoplevel'
eSetFilter : buildGUI: no visible global function definition for
  'tktitle<-'
eSetFilter : buildGUI: no visible global function definition for
  'tktext'
eSetFilter : buildGUI: no visible global function definition for
  'writeText'
eSetFilter : buildGUI: no visible global function definition for
  'tkconfigure'
eSetFilter : buildGUI: no visible global function definition for
  'tkpack'
eSetFilter : buildGUI: no visible global function definition for
  'tkframe'
eSetFilter : buildGUI: no visible global function definition for
  'tklabel'
eSetFilter : buildGUI: no visible global function definition for
  'makeViewer'
eSetFilter : buildGUI: no visible global function definition for
  'tkbind'
eSetFilter : buildGUI: no visible global function definition for
  'writeList'
eSetFilter : buildGUI: no visible global function definition for
  'tkbutton'
eSetFilter : buildGUI: no visible global function definition for
  'tkwait.window'
eSetFilter : buildGUI: no visible binding for global variable 'END'
getRdAsText: no visible global function definition for '.path.package'
isESet: no visible global function definition for 'tkmessageBox'
setESetArgs: no visible global function definition for 'tkdestroy'
setESetArgs : cancel: no visible global function definition for
  'tkdestroy'
setESetArgs : end: no visible global function definition for
  'tkdestroy'
setESetArgs: no visible global function definition for 'tktoplevel'
setESetArgs: no visible global function definition for 'tktitle<-'
setESetArgs: no visible global function definition for 'tkgrid'
setESetArgs: no visible global function definition for 'tklabel'
setESetArgs: no visible global function definition for 'tclVar'
setESetArgs: no visible global function definition for 'tkframe'
setESetArgs: no visible global function definition for 'makeViewer'
setESetArgs: no visible global function definition for 'writeText'
setESetArgs: no visible global function definition for 'tkconfigure'
setESetArgs: no visible global function definition for 'tkentry'
setESetArgs: no visible global function definition for 'tkbind'
setESetArgs: no visible global function definition for
  'tkgrid.configure'
setESetArgs: no visible global function definition for 'tkbutton'
setESetArgs: no visible global function definition for 'tkpack'
setESetArgs: no visible global function definition for 'tkwait.window'
setESetArgs: no visible global function definition for 'tclvalue'
showESet : end: no visible global function definition for 'tkdestroy'
showESet: no visible global function definition for 'tktoplevel'
showESet: no visible global function definition for 'tktitle<-'
showESet: no visible global function definition for 'tkframe'
showESet: no visible global function definition for 'makeViewer'
showESet: no visible global function definition for 'writeList'
showESet: no visible global function definition for 'tkpack'
showESet: no visible global function definition for 'tkbutton'
Undefined global functions or variables:
  .path.package END makeViewer tclVar tclvalue tkbind tkbutton
  tkconfigure tkcurselection tkdestroy tkentry tkframe tkget tkgrid
  tkgrid.configure tklabel tkmessageBox tkpack tktext tktitle<-
  tktoplevel tkwait.window writeList writeText
* 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 LazyData ... 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-3.14-bioc/R/library/genefilter/libs/i386/genefilter.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/genefilter/libs/x64/genefilter.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
rowFtests 4.95   0.13    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
rowFtests 7.25   0.16     7.4
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/genefilter.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/genefilter_1.76.0.tar.gz && rm -rf genefilter.buildbin-libdir && mkdir genefilter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genefilter.buildbin-libdir genefilter_1.76.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL genefilter_1.76.0.zip && rm genefilter_1.76.0.tar.gz genefilter_1.76.0.zip
###
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100  117k  100  117k    0     0   223k      0 --:--:-- --:--:-- --:--:--  224k

install for i386

* installing *source* package 'genefilter' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c half_range_mode.cpp -o half_range_mode.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nd.c -o nd.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pAUC.c -o pAUC.o
pAUC.c: In function 'pAUC':
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
     if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
        ~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rowPAUCs.c -o rowPAUCs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rowttests.c -o rowttests.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c ttest.f -o ttest.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genefilter.dll tmp.def half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/genefilter.buildbin-libdir/00LOCK-genefilter/00new/genefilter/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genefilter'
    finding HTML links ... done
    Anova                                   html  
    coxfilter                               html  
    cv                                      html  
    deprecated                              html  
    dist2                                   html  
    eSetFilter                              html  
    filter_volcano                          html  
    filtered_p                              html  
    filterfun                               html  
    findLargest                             html  
    gapFilter                               html  
    genefilter                              html  
    genefinder                              html  
    genescale                               html  
    half.range.mode                         html  
    kOverA                                  html  
    kappa_p                                 html  
    maxA                                    html  
    nsFilter                                html  
    pOverA                                  html  
    rejection_plot                          html  
    rowFtests                               html  
    rowROC-class                            html  
    rowSds                                  html  
    rowpAUCs                                html  
    shorth                                  html  
    tdata                                   html  
    ttest                                   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 'genefilter' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c half_range_mode.cpp -o half_range_mode.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nd.c -o nd.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pAUC.c -o pAUC.o
pAUC.c: In function 'pAUC':
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
     if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
        ~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rowPAUCs.c -o rowPAUCs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rowttests.c -o rowttests.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c ttest.f -o ttest.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genefilter.dll tmp.def half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/genefilter.buildbin-libdir/genefilter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefilter' as genefilter_1.76.0.zip
* DONE (genefilter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'genefilter' successfully unpacked and MD5 sums checked