BioC 3.4: CHECK report for netbenchmark on tokay1

Package: netbenchmark

Version: 1.6.0

Command: rm -rf netbenchmark.buildbin-libdir netbenchmark.Rcheck && mkdir netbenchmark.buildbin-libdir netbenchmark.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netbenchmark.buildbin-libdir netbenchmark_1.6.0.tar.gz >netbenchmark.Rcheck\00install.out 2>&1 && cp netbenchmark.Rcheck\00install.out netbenchmark-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=netbenchmark.buildbin-libdir --install="check:netbenchmark-install.out" --force-multiarch --no-vignettes --timings netbenchmark_1.6.0.tar.gz

StartedAt: 2017-04-14 23:47:46 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:50:36 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 170.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netbenchmark.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf netbenchmark.buildbin-libdir netbenchmark.Rcheck && mkdir netbenchmark.buildbin-libdir netbenchmark.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=netbenchmark.buildbin-libdir netbenchmark_1.6.0.tar.gz >netbenchmark.Rcheck\00install.out 2>&1 && cp netbenchmark.Rcheck\00install.out netbenchmark-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=netbenchmark.buildbin-libdir --install="check:netbenchmark-install.out" --force-multiarch --no-vignettes --timings netbenchmark_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'netbenchmark/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'netbenchmark' version '1.6.0'
* 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 'netbenchmark' can be installed ... OK
* 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
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addnoise: no visible global function definition for 'sd'
.addnoise: no visible global function definition for 'runif'
.addnoise: no visible global function definition for 'rnorm'
.addnoise: no visible global function definition for 'rlnorm'
.cont: no visible global function definition for 'sd'
.cont: no visible global function definition for 'rnorm'
.cont: no visible global function definition for 'rlnorm'
.get.pr.plot: no visible global function definition for 'dev.new'
.get.pr.plot: no visible global function definition for 'par'
.get.pr.plot: no visible global function definition for 'rainbow'
.get.pr.plot: no visible global function definition for 'plot'
.get.pr.plot: no visible global function definition for 'points'
.get.pr.plot: no visible global function definition for 'legend'
.get.weight.matrix : <anonymous>: no visible global function definition
  for 'sd'
.get.weight.matrix: no visible global function definition for
  'flush.console'
.pgfplots.export: no visible global function definition for
  'write.table'
.results.plot: no visible global function definition for 'dev.new'
.results.plot: no visible global function definition for 'par'
.results.plot: no visible global function definition for 'boxplot'
.results.plot: no visible global function definition for 'title'
GeneNet.wrap: no visible global function definition for 'as'
datasource.subsample: no visible global function definition for 'runif'
datasource.subsample: no visible binding for global variable 'sd'
datasource.subsample: no visible global function definition for 'rnorm'
datasource.subsample: no visible global function definition for
  'rlnorm'
experiments.bench: no visible global function definition for 'runif'
experiments.bench: no visible global function definition for
  'wilcox.test'
mutrank.wrap: no visible global function definition for 'cor'
netbenchmark: no visible global function definition for 'runif'
netbenchmark: no visible global function definition for 'wilcox.test'
netbenchmark.data: no visible global function definition for 'rainbow'
netbenchmark.data: no visible global function definition for 'runif'
noise.bench: no visible global function definition for 'runif'
noise.bench: no visible binding for global variable 'sd'
noise.bench: no visible global function definition for 'rnorm'
noise.bench: no visible global function definition for 'rlnorm'
noise.bench: no visible global function definition for 'wilcox.test'
pcit.wrap: no visible global function definition for 'cor'
pr.plot: no visible global function definition for 'dev.new'
pr.plot: no visible global function definition for 'plot'
pr.plot: no visible global function definition for 'dev.set'
pr.plot: no visible global function definition for 'points'
pr.plot: no visible global function definition for 'dev.cur'
roc.plot: no visible global function definition for 'dev.new'
roc.plot: no visible global function definition for 'plot'
roc.plot: no visible global function definition for 'dev.set'
roc.plot: no visible global function definition for 'points'
roc.plot: no visible global function definition for 'lines'
roc.plot: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  as boxplot cor dev.cur dev.new dev.set flush.console legend lines par
  plot points rainbow rlnorm rnorm runif sd title wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new", "dev.set", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "points", "title")
  importFrom("methods", "as")
  importFrom("stats", "cor", "rlnorm", "rnorm", "runif", "sd",
             "wilcox.test")
  importFrom("utils", "flush.console", "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 ... WARNING
Codoc mismatches from documentation object 'netbenchmark':
netbenchmark
  Code: function(methods = "all.fast", datasources.names = "all",
                 experiments = 150, eval = "AUPR", no.topedges = 20,
                 datasets.num = 5, local.noise = 20, global.noise = 0,
                 noiseType = "normal", sym = TRUE, plot = FALSE, seed =
                 NULL, verbose = TRUE, return.nets = FALSE)
  Docs: function(methods = "all.fast", datasources.names = "all",
                 experiments = 150, eval = "AUPR", no.topedges = 20,
                 datasets.num = 5, local.noise = 20, global.noise = 0,
                 noiseType = "normal", sym = TRUE, plot = FALSE, seed =
                 NULL, verbose = TRUE)
  Argument names in code not in docs:
    return.nets

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'netbenchmark':
  'return.nets'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 'C:/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.buildbin-libdir/netbenchmark/libs/i386/netbenchmark.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
Genie3.wrap       9.84   0.03    9.90
netbenchmark.data 9.25   0.01    9.27
netbenchmark      7.75   0.03    7.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
netbenchmark.data 8.36   0.02    8.37
Genie3.wrap       7.73   0.00    7.75
netbenchmark      6.98   0.00    6.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'netbenchmark' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c netbenchmark_init.c -o netbenchmark_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c rate.cpp -o rate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c zsc.cpp -o zsc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o netbenchmark.dll tmp.def RcppExports.o netbenchmark_init.o rate.o zsc.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.buildbin-libdir/netbenchmark/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 'netbenchmark' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c netbenchmark_init.c -o netbenchmark_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c rate.cpp -o rate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c zsc.cpp -o zsc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o netbenchmark.dll tmp.def RcppExports.o netbenchmark_init.o rate.o zsc.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.buildbin-libdir/netbenchmark/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'netbenchmark' as netbenchmark_1.6.0.zip
* DONE (netbenchmark)

name	user	system	elapsed
GeneNet.wrap	0.39	0.00	0.46
Genie3.wrap	9.84	0.03	9.90
RegistrerWrapper	0	0	0
aracne.wrap	0	0	0
c3net.wrap	0.02	0.00	0.02
clr.wrap	0	0	0
comp.metr	1.11	0.04	1.84
datasource.subsample	0.51	0.00	0.52
evaluate	1.92	0.02	1.94
experiments.bench	1.21	0.02	1.26
mrnet.wrap	0	0	0
mrnetb.wrap	0	0	0
mutrank.wrap	0.02	0.00	0.01
netbenchmark-package	0	0	0
netbenchmark	7.75	0.03	7.78
netbenchmark.data	9.25	0.01	9.27
noise.bench	2.09	0.00	2.09
ntb_globals	0	0	0
pcit.wrap	0.02	0.00	0.02
rate	0	0	0
zsc	0	0	0
zscore.wrap	0	0	0

name	user	system	elapsed
GeneNet.wrap	0.49	0.02	0.50
Genie3.wrap	7.73	0.00	7.75
RegistrerWrapper	0	0	0
aracne.wrap	0.02	0.00	0.35
c3net.wrap	0.15	0.00	0.15
clr.wrap	0.02	0.00	0.02
comp.metr	1.09	0.00	1.09
datasource.subsample	0.52	0.00	0.52
evaluate	2.23	0.01	2.25
experiments.bench	1.23	0.00	1.23
mrnet.wrap	0	0	0
mrnetb.wrap	0.02	0.00	0.02
mutrank.wrap	0	0	0
netbenchmark-package	0	0	0
netbenchmark	6.98	0.00	6.98
netbenchmark.data	8.36	0.02	8.37
noise.bench	2.09	0.00	2.09
ntb_globals	0	0	0
pcit.wrap	0	0	0
rate	0	0	0
zsc	0	0	0
zscore.wrap	0	0	0