BioC 3.3: CHECK report for iBBiG on moscato2

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### Running command:
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###   rm -rf iBBiG.buildbin-libdir iBBiG.Rcheck && mkdir iBBiG.buildbin-libdir iBBiG.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iBBiG.buildbin-libdir iBBiG_1.16.0.tar.gz >iBBiG.Rcheck\00install.out 2>&1 && cp iBBiG.Rcheck\00install.out iBBiG-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=iBBiG.buildbin-libdir --install="check:iBBiG-install.out" --force-multiarch --no-vignettes --timings iBBiG_1.16.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/iBBiG.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iBBiG/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBBiG' version '1.16.0'
* 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 'iBBiG' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'biclust' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSignal: no visible global function definition for 'runif'
iBBiG: no visible global function definition for 'new'
makeArtificial: no visible global function definition for 'runif'
makeArtificial: no visible global function definition for 'new'
Clusterscores,iBBiG: no visible global function definition for 'slot'
Clusterscores<-,iBBiG: no visible global function definition for
  'slot<-'
Clusterscores<-,iBBiG: no visible global function definition for
  'validObject'
Number,iBBiG: no visible global function definition for 'slot'
Number<-,iBBiG: no visible global function definition for 'slot<-'
Number<-,iBBiG: no visible global function definition for 'validObject'
NumberxCol,iBBiG: no visible global function definition for 'slot'
NumberxCol<-,iBBiG: no visible global function definition for 'slot<-'
NumberxCol<-,iBBiG: no visible global function definition for
  'validObject'
Parameters,iBBiG: no visible global function definition for 'slot'
Parameters<-,iBBiG: no visible global function definition for 'slot<-'
Parameters<-,iBBiG: no visible global function definition for
  'validObject'
RowScorexNumber,iBBiG: no visible global function definition for 'slot'
RowScorexNumber<-,iBBiG: no visible global function definition for
  'slot<-'
RowScorexNumber<-,iBBiG: no visible global function definition for
  'validObject'
RowxNumber,iBBiG: no visible global function definition for 'slot'
RowxNumber<-,iBBiG: no visible global function definition for 'slot<-'
RowxNumber<-,iBBiG: no visible global function definition for
  'validObject'
Seeddata,iBBiG: no visible global function definition for 'slot'
Seeddata<-,iBBiG: no visible global function definition for 'slot<-'
Seeddata<-,iBBiG: no visible global function definition for
  'validObject'
analyzeClust,Biclust-iBBiG: no visible global function definition for
  'as'
analyzeClust,list-iBBiG: no visible global function definition for
  'new'
coerce,Biclust-iBBiG: no visible global function definition for 'new'
info,iBBiG: no visible global function definition for 'slot'
info<-,iBBiG: no visible global function definition for 'slot<-'
info<-,iBBiG: no visible global function definition for 'validObject'
plot,iBBiG-ANY: no visible global function definition for 'layout'
plot,iBBiG-ANY: no visible global function definition for 'colors'
plot,iBBiG-ANY: no visible global function definition for 'image'
plot,iBBiG-ANY: no visible global function definition for 'legend'
plot,iBBiG-ANY: no visible binding for global variable 'title'
plot,iBBiG-ANY: no visible global function definition for 'title'
plot,iBBiG-ANY: no visible global function definition for 'barplot'
Undefined global functions or variables:
  as barplot colors image layout legend new runif slot slot<- title
  validObject
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "barplot", "image", "layout", "legend", "title")
  importFrom("methods", "as", "new", "slot", "slot<-", "validObject")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 'E:/biocbld/bbs-3.3-bioc/meat/iBBiG.buildbin-libdir/iBBiG/libs/i386/iBBiG.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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
iBBiG         47.66   0.09   47.76
iBBiG-package 42.96   0.13   43.10
iBBiG-class   40.25   0.03   40.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
iBBiG-package 45.95   0.00   45.94
iBBiG         40.81   0.11   40.92
iBBiG-class   40.48   0.05   40.53
* 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/iBBiG.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'iBBiG' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_iBBiG.c -o R_init_iBBiG.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c iBBiG.c -o iBBiG.o
iBBiG.c: In function 'clusterCovsC':
iBBiG.c:300:6: warning: implicit declaration of function 'time' [-Wimplicit-function-declaration]
      srand((unsigned)time(NULL));     
      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o iBBiG.dll tmp.def R_init_iBBiG.o iBBiG.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/iBBiG.buildbin-libdir/iBBiG/libs/i386
** R
** 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 'iBBiG' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_iBBiG.c -o R_init_iBBiG.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c iBBiG.c -o iBBiG.o
iBBiG.c: In function 'clusterCovsC':
iBBiG.c:300:6: warning: implicit declaration of function 'time' [-Wimplicit-function-declaration]
      srand((unsigned)time(NULL));     
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o iBBiG.dll tmp.def R_init_iBBiG.o iBBiG.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/iBBiG.buildbin-libdir/iBBiG/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iBBiG' as iBBiG_1.16.0.zip
* DONE (iBBiG)

BioC 3.3: CHECK report for iBBiG on moscato2

Summary

Command output

name	user	system	elapsed
iBBiG-class	40.25	0.03	40.28
iBBiG-package	42.96	0.13	43.10
iBBiG	47.66	0.09	47.76
makeArtificial	1.07	0.05	1.13