Package: netbenchmark

Version: 1.12.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:netbenchmark.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings netbenchmark_1.12.0.tar.gz

StartedAt: 2018-10-16 02:20:43 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:22:15 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 91.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netbenchmark.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:netbenchmark.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings netbenchmark_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/netbenchmark.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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’
.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 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", "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 ... WARNING
Undocumented code objects:
  ‘_netbenchmark_rate’ ‘_netbenchmark_zsc’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
netbenchmark      15.300  0.008  15.319
Genie3.wrap       13.420  0.008  13.443
netbenchmark.data 12.924  0.000  12.935
* 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: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/netbenchmark.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL netbenchmark
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘netbenchmark’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c netbenchmark_init.c -o netbenchmark_init.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rate.cpp -o rate.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c zsc.cpp -o zsc.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o netbenchmark.so RcppExports.o netbenchmark_init.o rate.o zsc.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/netbenchmark/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netbenchmark)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("netbenchmark")


RUNIT TEST PROTOCOL -- Tue Oct 16 02:22:13 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
netbenchmark RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.584   0.080   1.669 

name	user	system	elapsed
GeneNet.wrap	0.464	0.028	0.558
Genie3.wrap	13.420	0.008	13.443
RegistrerWrapper	0.000	0.000	0.001
aracne.wrap	0.008	0.000	0.005
c3net.wrap	0.016	0.000	0.017
clr.wrap	0.008	0.000	0.004
comp.metr	0.480	0.004	0.507
datasource.subsample	0.828	0.000	0.829
evaluate	1.068	0.000	1.068
experiments.bench	1.088	0.000	1.113
mrnet.wrap	0.000	0.004	0.004
mrnetb.wrap	0.008	0.000	0.006
mutrank.wrap	0.004	0.000	0.003
netbenchmark-package	0.000	0.000	0.001
netbenchmark	15.300	0.008	15.319
netbenchmark.data	12.924	0.000	12.935
noise.bench	1.456	0.000	1.455
ntb_globals	0	0	0
pcit.wrap	0.008	0.000	0.005
rate	0.000	0.000	0.001
zsc	0.004	0.000	0.001
zscore.wrap	0.000	0.000	0.002