BioC 3.5: CHECK report for netbenchmark on toluca2

Package: netbenchmark

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbenchmark_1.7.0.tar.gz

StartedAt: 2017-04-23 07:19:35 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:21:36 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 121.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netbenchmark.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbenchmark_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/netbenchmark.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netbenchmark/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netbenchmark’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
netbenchmark      10.280  0.218  11.086
Genie3.wrap        9.830  0.104  10.154
netbenchmark.data  9.755  0.131  10.007
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/netbenchmark.Rcheck/00check.log’
for details.

* installing *source* package ‘netbenchmark’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c netbenchmark_init.c -o netbenchmark_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rate.cpp -o rate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c zsc.cpp -o zsc.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o netbenchmark.so RcppExports.o netbenchmark_init.o rate.o zsc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/netbenchmark.Rcheck/netbenchmark/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netbenchmark)

name	user	system	elapsed
GeneNet.wrap	1.077	0.028	1.110
Genie3.wrap	9.830	0.104	10.154
RegistrerWrapper	0.001	0.000	0.001
aracne.wrap	0.009	0.002	0.011
c3net.wrap	0.025	0.000	0.025
clr.wrap	0.042	0.000	0.043
comp.metr	1.040	0.046	1.137
datasource.subsample	0.936	0.026	0.962
evaluate	1.898	0.035	1.941
experiments.bench	2.076	0.025	2.140
mrnet.wrap	0.007	0.000	0.007
mrnetb.wrap	0.007	0.000	0.008
mutrank.wrap	0.006	0.000	0.007
netbenchmark-package	0.001	0.000	0.001
netbenchmark	10.280	0.218	11.086
netbenchmark.data	9.755	0.131	10.007
noise.bench	1.965	0.036	2.011
ntb_globals	0.001	0.000	0.001
pcit.wrap	0.006	0.000	0.006
rate	0.003	0.000	0.002
zsc	0.001	0.001	0.001
zscore.wrap	0.002	0.000	0.002