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BioC 3.4: CHECK report for netbenchmark on morelia

This page was generated on 2017-04-15 16:26:20 -0400 (Sat, 15 Apr 2017).

Package 834/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbenchmark 1.6.0
Pau Bellot
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/netbenchmark
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: netbenchmark
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings netbenchmark_1.6.0.tar.gz
StartedAt: 2017-04-15 05:37:16 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 05:39:05 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 109.2 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/netbenchmark.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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 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      11.524  0.230  11.828
netbenchmark.data  9.953  0.123  10.087
Genie3.wrap        9.709  0.072   9.791
* 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-3.4-bioc/meat/netbenchmark.Rcheck/00check.log’
for details.


netbenchmark.Rcheck/00install.out:

* installing *source* package ‘netbenchmark’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rate.cpp -o rate.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/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-3.4-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)

netbenchmark.Rcheck/netbenchmark-Ex.timings:

nameusersystemelapsed
GeneNet.wrap0.5200.0170.620
Genie3.wrap9.7090.0729.791
RegistrerWrapper0.0010.0000.002
aracne.wrap0.0050.0010.029
c3net.wrap0.0230.0000.023
clr.wrap0.0060.0000.005
comp.metr1.1740.0611.286
datasource.subsample0.7690.0180.787
evaluate2.2650.0412.307
experiments.bench1.2340.0131.298
mrnet.wrap0.0060.0000.007
mrnetb.wrap0.0090.0010.009
mutrank.wrap0.0070.0000.007
netbenchmark-package0.0000.0000.001
netbenchmark11.524 0.23011.828
netbenchmark.data 9.953 0.12310.087
noise.bench2.1480.0272.177
ntb_globals0.0010.0000.001
pcit.wrap0.0060.0010.007
rate0.0020.0000.003
zsc0.0010.0000.001
zscore.wrap0.0020.0000.002