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CHECK report for netbenchmark on veracruz1

This page was generated on 2018-04-12 13:40:28 -0400 (Thu, 12 Apr 2018).

Package 934/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbenchmark 1.10.0
Pau Bellot
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/netbenchmark
Branch: RELEASE_3_6
Last Commit: 81fcf3d
Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: netbenchmark
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbenchmark_1.10.0.tar.gz
StartedAt: 2018-04-12 07:02:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:04:33 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 110.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: netbenchmark.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbenchmark_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/netbenchmark.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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
Genie3.wrap       10.121  0.068  10.310
netbenchmark.data  9.468  0.105   9.716
netbenchmark       8.737  0.166   9.038
* 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-3.6-bioc/meat/netbenchmark.Rcheck/00check.log’
for details.



Installation output

netbenchmark.Rcheck/00install.out

* 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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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-3.6-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)

Tests output

netbenchmark.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Thu Apr 12 07:04:28 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 
  2.396   0.130   2.543 

Example timings

netbenchmark.Rcheck/netbenchmark-Ex.timings

nameusersystemelapsed
GeneNet.wrap1.0450.0261.082
Genie3.wrap10.121 0.06810.310
RegistrerWrapper0.0010.0000.001
aracne.wrap0.0060.0000.008
c3net.wrap0.0230.0000.024
clr.wrap0.0340.0010.035
comp.metr1.0740.0351.135
datasource.subsample0.8050.0240.848
evaluate1.5230.0261.565
experiments.bench1.7470.0111.784
mrnet.wrap0.0060.0000.006
mrnetb.wrap0.0070.0000.007
mutrank.wrap0.0030.0010.003
netbenchmark-package0.0010.0000.001
netbenchmark8.7370.1669.038
netbenchmark.data9.4680.1059.716
noise.bench1.5830.0171.620
ntb_globals0.0010.0000.001
pcit.wrap0.0050.0010.005
rate0.0020.0000.002
zsc000
zscore.wrap0.0010.0000.001