BioC 3.5: CHECK report for CellNOptR on tokay2

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### Running command:
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###   rm -rf CellNOptR.buildbin-libdir CellNOptR.Rcheck && mkdir CellNOptR.buildbin-libdir CellNOptR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CellNOptR.buildbin-libdir CellNOptR_1.22.0.tar.gz >CellNOptR.Rcheck\00install.out 2>&1 && cp CellNOptR.Rcheck\00install.out CellNOptR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CellNOptR.buildbin-libdir --install="check:CellNOptR-install.out" --force-multiarch --no-vignettes --timings CellNOptR_1.22.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CellNOptR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellNOptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellNOptR' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RBGL' 'graph' 'hash' 'ggplot2' 'RCurl' 'Rgraphviz' 'XML'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'CellNOptR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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' calls to packages already attached by Depends:
  'RBGL' 'RCurl' 'Rgraphviz' 'XML' 'hash'
  Please remove these calls from your code.
'library' or 'require' call to 'igraph' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'RCurl' 'Rgraphviz' 'XML' 'ggplot2' 'hash' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.error.bar: no visible global function definition for 'arrows'
CNORwrap: no visible global function definition for 'pdf'
CNORwrap: no visible global function definition for 'dev.off'
CNOdata: no visible global function definition for 'getURL'
CNOlist: no visible global function definition for 'new'
createEdgeAttrs: no visible global function definition for 'rgb'
expandGates: no visible global function definition for 'combn'
findNONC : modeltoGraphNEL: no visible global function definition for
  'new'
gaBinaryT1: no visible global function definition for 'runif'
gaBinaryT1: no visible global function definition for 'hash'
gaBinaryT1 : getObj: no visible global function definition for
  'has.key'
gaBinaryT2: no visible global function definition for 'runif'
gaBinaryT2: no visible global function definition for 'hash'
gaBinaryT2 : getObj: no visible global function definition for
  'has.key'
gaBinaryTN: no visible global function definition for 'runif'
gaBinaryTN: no visible global function definition for 'hash'
gaBinaryTN : getObj: no visible global function definition for
  'has.key'
graph2sif: no visible global function definition for 'write.table'
makeCNOlist: no visible binding for global variable 'var'
mapBack : SearchPath: no visible binding for global variable 'tail'
mapBack: no visible global function definition for 'write.table'
model2igraph: no visible global function definition for
  'igraph.from.graphNEL'
plotCNOlist: no visible global function definition for 'par'
plotCNOlist: no visible global function definition for 'text'
plotCNOlist: no visible global function definition for 'lines'
plotCNOlist: no visible global function definition for 'axis'
plotCNOlist: no visible global function definition for 'image'
plotCNOlist2: no visible global function definition for 'ggplot'
plotCNOlist2: no visible global function definition for 'aes'
plotCNOlist2: no visible binding for global variable 'values'
plotCNOlist2: no visible global function definition for 'geom_point'
plotCNOlist2: no visible global function definition for 'geom_line'
plotCNOlist2: no visible global function definition for 'xlab'
plotCNOlist2: no visible global function definition for 'ylab'
plotCNOlist2: no visible global function definition for 'facet_grid'
plotCNOlist2: no visible global function definition for 'theme_bw'
plotCNOlist2: no visible global function definition for 'theme'
plotCNOlist2: no visible global function definition for 'element_text'
plotCNOlist2: no visible global function definition for 'element_rect'
plotCNOlist2: no visible global function definition for 'ylim'
plotCNOlistLarge: no visible global function definition for 'par'
plotCNOlistLarge: no visible global function definition for 'dev.new'
plotCNOlistLarge: no visible global function definition for 'text'
plotCNOlistLarge: no visible global function definition for 'lines'
plotCNOlistLarge: no visible global function definition for 'axis'
plotCNOlistLarge: no visible global function definition for 'image'
plotCNOlistLargePDF: no visible global function definition for 'pdf'
plotCNOlistLargePDF: no visible global function definition for
  'dev.off'
plotCNOlistPDF: no visible global function definition for 'pdf'
plotCNOlistPDF: no visible global function definition for 'dev.off'
plotFit: no visible global function definition for 'par'
plotFit: no visible global function definition for 'pdf'
plotFit: no visible global function definition for 'dev.off'
plotModel: no visible global function definition for 'pdf'
plotModel: no visible global function definition for 'png'
plotModel: no visible global function definition for 'svg'
plotModel: no visible global function definition for 'read.table'
plotModel: no visible global function definition for 'new'
plotModel: no visible global function definition for
  'installed.packages'
plotModel: no visible global function definition for 'layoutGraph'
plotModel: no visible global function definition for 'renderGraph'
plotModel: no visible global function definition for 'toDot'
plotModel: no visible global function definition for 'dev.off'
plotOptimResults: no visible global function definition for 'par'
plotOptimResults: no visible global function definition for 'text'
plotOptimResults: no visible global function definition for 'rect'
plotOptimResults: no visible global function definition for 'points'
plotOptimResults: no visible global function definition for 'lines'
plotOptimResults: no visible global function definition for 'axis'
plotOptimResults: no visible global function definition for 'image'
plotOptimResultsPDF: no visible global function definition for 'pdf'
plotOptimResultsPDF: no visible global function definition for
  'dev.off'
plotOptimResultsPan: no visible global function definition for 'par'
plotOptimResultsPan: no visible global function definition for
  'split.screen'
plotOptimResultsPan: no visible global function definition for
  'heat.colors'
plotOptimResultsPan: no visible global function definition for 'screen'
plotOptimResultsPan: no visible global function definition for 'text'
plotOptimResultsPan: no visible global function definition for 'rect'
plotOptimResultsPan: no visible global function definition for 'lines'
plotOptimResultsPan: no visible global function definition for 'points'
plotOptimResultsPan: no visible global function definition for 'axis'
plotOptimResultsPan: no visible global function definition for 'image'
plotOptimResultsPan: no visible global function definition for
  'plot.new'
plotOptimResultsPan: no visible global function definition for
  'segments'
plotOptimResultsPan: no visible global function definition for
  'close.screen'
plotOptimResultsPan: no visible global function definition for
  'dev.off'
randomizeCNOlist: no visible global function definition for 'rnorm'
randomizeCNOlist: no visible global function definition for 'runif'
readMIDAS: no visible global function definition for 'count.fields'
readMIDAS: no visible global function definition for 'read.csv'
readMIDAS: no visible global function definition for 'read.table'
readSBMLQual: no visible global function definition for 'xmlTreeParse'
readSBMLQual: no visible global function definition for 'xmlRoot'
readSBMLQual: no visible global function definition for 'xmlChildren'
readSBMLQual: no visible global function definition for 'xmlApply'
readSBMLQual : <anonymous>: no visible global function definition for
  'xmlGetAttr'
readSBMLQual: no visible global function definition for 'write.table'
readSIF: no visible global function definition for 'read.table'
sif2graph: no visible global function definition for 'read.table'
sif2graph: no visible global function definition for 'new'
writeDot : modeltoGraphNEL: no visible global function definition for
  'new'
writeMIDAS: no visible global function definition for 'write.table'
writeNetworkW: no visible global function definition for 'write.table'
writeSIF: no visible global function definition for 'write.table'
writeScaffoldW: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aes arrows axis close.screen combn count.fields dev.new dev.off
  element_rect element_text facet_grid geom_line geom_point getURL
  ggplot has.key hash heat.colors igraph.from.graphNEL image
  installed.packages layoutGraph lines new par pdf plot.new png points
  read.csv read.table rect renderGraph rgb rnorm runif screen segments
  split.screen svg tail text theme theme_bw toDot values var
  write.table xlab xmlApply xmlChildren xmlGetAttr xmlRoot xmlTreeParse
  ylab ylim
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf",
             "png", "rgb", "svg")
  importFrom("graphics", "arrows", "axis", "close.screen", "image",
             "lines", "par", "plot.new", "points", "rect", "screen",
             "segments", "split.screen", "text")
  importFrom("methods", "new")
  importFrom("stats", "rnorm", "runif", "var")
  importFrom("utils", "combn", "count.fields", "installed.packages",
             "read.csv", "read.table", "tail", "write.table")
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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/CellNOptR.buildbin-libdir/CellNOptR/libs/i386/CellNOptR.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 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' ... ERROR
Running examples in 'CellNOptR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CNOdata
> ### Title: Get data from a CellNOpt data repository
> ### Aliases: CNOdata
> 
> ### ** Examples
> 
> readSIF(CNOdata("PKN-ToyMMB.sif"))
Error in matrix(sif, ncol = 3, byrow = TRUE) : 
  'data' must be of a vector type, was 'NULL'
Calls: readSIF -> matrix
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'CellNOptR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CNOdata
> ### Title: Get data from a CellNOpt data repository
> ### Aliases: CNOdata
> 
> ### ** Examples
> 
> readSIF(CNOdata("PKN-ToyMMB.sif"))
Error in matrix(sif, ncol = 3, byrow = TRUE) : 
  'data' must be of a vector type, was 'NULL'
Calls: readSIF -> matrix
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_manySteadyStates.R'
  Running 'test_priorBitString.R'
  Running 'test_simulateTN.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_manySteadyStates.R'
  Running 'test_priorBitString.R'
  Running 'test_simulateTN.R'
 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: 2 ERRORs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CellNOptR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'CellNOptR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=core2 -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
  int nReacs = INTEGER(nReacs_in)[0];
      ^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
  int selCounter = 0;
      ^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
  int selection[40];
      ^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
  int or_max = 0;
      ^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
  int curr_max = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=core2 -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O3 -Wall  -std=gnu99 -mtune=core2 -c simulatorTN.c -o simulatorTN.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/i386
** R
** data
** 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 'CellNOptR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=core2 -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
  int nReacs = INTEGER(nReacs_in)[0];
      ^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
  int selCounter = 0;
      ^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
  int selection[40];
      ^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
  int or_max = 0;
      ^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
  int curr_max = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=core2 -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I./include    -O2 -Wall  -std=gnu99 -mtune=core2 -c simulatorTN.c -o simulatorTN.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellNOptR' as CellNOptR_1.22.0.zip
* DONE (CellNOptR)

name	user	system	elapsed
CNORbool	1.40	0.02	1.42

name	user	system	elapsed
CNORbool	1.93	0.03	2.00

BioC 3.5: CHECK report for CellNOptR on tokay2

Summary

Command output