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BioC 3.5: CHECK report for genefilter on tokay2

This page was generated on 2017-08-16 13:18:27 -0400 (Wed, 16 Aug 2017).

Package 511/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefilter 1.58.1
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/genefilter
Last Changed Rev: 129423 / Revision: 131943
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genefilter
Version: 1.58.1
Command: rm -rf genefilter.buildbin-libdir genefilter.Rcheck && mkdir genefilter.buildbin-libdir genefilter.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genefilter.buildbin-libdir genefilter_1.58.1.tar.gz >genefilter.Rcheck\00install.out 2>&1 && cp genefilter.Rcheck\00install.out genefilter-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genefilter.buildbin-libdir --install="check:genefilter-install.out" --force-multiarch --no-vignettes --timings genefilter_1.58.1.tar.gz
StartedAt: 2017-08-15 23:55:31 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:58:53 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 201.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: genefilter.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genefilter.buildbin-libdir genefilter.Rcheck && mkdir genefilter.buildbin-libdir genefilter.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genefilter.buildbin-libdir genefilter_1.58.1.tar.gz >genefilter.Rcheck\00install.out 2>&1 && cp genefilter.Rcheck\00install.out genefilter-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genefilter.buildbin-libdir --install="check:genefilter-install.out" --force-multiarch --no-vignettes --timings genefilter_1.58.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/genefilter.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.58.1'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
.findDBMeta: no visible global function definition for 'dbmeta'
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'
filter_volcano: no visible global function definition for 'segments'
filter_volcano: no visible global function definition for 'legend'
filtered_p: no visible global function definition for 'p.adjust'
isESet: no visible global function definition for 'tkmessageBox'
kappa_p: no visible global function definition for 'qt'
rejection_plot: no visible global function definition for 'rainbow'
rejection_plot : <anonymous>: no visible global function definition for
  'na.omit'
rejection_plot : <anonymous>: no visible global function definition for
  'stepfun'
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:
  END dbmeta legend makeViewer na.omit p.adjust qt rainbow segments
  stepfun tclVar tclvalue tkbind tkbutton tkconfigure tkcurselection
  tkdestroy tkentry tkframe tkget tkgrid tkgrid.configure tklabel
  tkmessageBox tkpack tktext tktitle<- tktoplevel tkwait.window
  writeList writeText
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "segments")
  importFrom("stats", "na.omit", "p.adjust", "qt", "stepfun")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'rowROC,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.5-bioc/meat/genefilter.buildbin-libdir/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)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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
Examples with CPU or elapsed time > 5s
          user system elapsed
rowFtests 8.43   0.09    8.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
rowFtests 8.07   0.05     8.1
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/genefilter.Rcheck/00check.log'
for details.


genefilter.Rcheck/00install.out:


install for i386

* installing *source* package 'genefilter' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c half_range_mode.cpp -o half_range_mode.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nd.c -o nd.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rowPAUCs.c -o rowPAUCs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rowttests.c -o rowttests.o
C:/Rtools/mingw_32/bin/gfortran      -O3  -mtune=core2 -c ttest.f -o ttest.o
C:/Rtools/mingw_32/bin/g++ -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:/local323/lib/i386 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/genefilter.buildbin-libdir/genefilter/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'genefilter' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c half_range_mode.cpp -o half_range_mode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nd.c -o nd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rowPAUCs.c -o rowPAUCs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rowttests.c -o rowttests.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=core2 -c ttest.f -o ttest.o
C:/Rtools/mingw_64/bin/g++ -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:/local323/lib/x64 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/genefilter.buildbin-libdir/genefilter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genefilter' as genefilter_1.58.1.zip
* DONE (genefilter)

genefilter.Rcheck/examples_i386/genefilter-Ex.timings:

nameusersystemelapsed
Anova0.010.000.01
coxfilter0.050.000.05
cv000
dist20.000.010.01
eSetFilter000
filter_volcano000
filtered_p000
filterfun0.040.000.03
findLargest0.750.050.80
gapFilter0.020.000.02
genefilter000
genefinder0.080.050.13
genescale000
half.range.mode3.780.013.79
kOverA000
kappa_p000
maxA000
nsFilter0.530.020.55
pOverA000
rejection_plot000
rowFtests8.430.098.52
rowROC-class0.060.020.08
rowSds000
rowpAUCs1.300.041.35
shorth000
tdata000
ttest0.010.000.02

genefilter.Rcheck/examples_x64/genefilter-Ex.timings:

nameusersystemelapsed
Anova0.060.000.06
coxfilter0.070.000.06
cv000
dist2000
eSetFilter000
filter_volcano000
filtered_p000
filterfun000
findLargest1.140.081.22
gapFilter0.010.000.02
genefilter000
genefinder0.110.030.14
genescale000
half.range.mode3.350.003.34
kOverA000
kappa_p000
maxA000
nsFilter0.650.010.68
pOverA000
rejection_plot000
rowFtests8.070.058.10
rowROC-class0.070.000.08
rowSds000
rowpAUCs1.540.001.53
shorth0.010.000.02
tdata000
ttest0.030.000.03