Package: netbenchmark

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings netbenchmark_1.16.0.tar.gz

StartedAt: 2019-10-16 05:34:45 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:38:00 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 194.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netbenchmark.Rcheck

Warnings: 4

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings netbenchmark_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/netbenchmark.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.16.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/GeneNet.wrap.Rd:48: file link 'GeneNet-package' in package 'GeneNet' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/datasource.subsample.Rd:35: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:48: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:77: file link 'rnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:78: file link 'rlnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/netbenchmark.Rd:40: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/noise.bench.Rd:46: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/netbenchmark.Rcheck/00install.out' for details.
* 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
* 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
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/netbenchmark/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
netbenchmark.data 15.33   0.32   15.64
netbenchmark      15.08   0.39   15.47
Genie3.wrap       13.99   0.22   14.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Genie3.wrap       12.81   0.36   13.19
netbenchmark      10.98   0.46   11.44
netbenchmark.data 10.20   0.34   10.54
* 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: 4 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/netbenchmark.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/netbenchmark_1.16.0.tar.gz && rm -rf netbenchmark.buildbin-libdir && mkdir netbenchmark.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=netbenchmark.buildbin-libdir netbenchmark_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL netbenchmark_1.16.0.zip && rm netbenchmark_1.16.0.tar.gz netbenchmark_1.16.0.zip
###
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100 33894  100 33894    0     0   277k      0 --:--:-- --:--:-- --:--:--  295k

install for i386

* installing *source* package 'netbenchmark' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c netbenchmark_init.c -o netbenchmark_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rate.cpp -o rate.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/netbenchmark.buildbin-libdir/00LOCK-netbenchmark/00new/netbenchmark/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'netbenchmark'
    finding HTML links ... done
    GeneNet.wrap                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/GeneNet.wrap.Rd:48: file link 'GeneNet-package' in package 'GeneNet' does not exist and so has been treated as a topic
    Genie3.wrap                             html  
    RegistrerWrapper                        html  
    aracne.wrap                             html  
    c3net.wrap                              html  
    clr.wrap                                html  
    comp.metr                               html  
    datasource.subsample                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/datasource.subsample.Rd:35: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
    evaluate                                html  
    experiments.bench                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:48: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:77: file link 'rnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/experiments.bench.Rd:78: file link 'rlnorm' in package 'stats' does not exist and so has been treated as a topic
    mrnet.wrap                              html  
    mrnetb.wrap                             html  
    mutrank.wrap                            html  
    netbenchmark-package                    html  
    netbenchmark                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/netbenchmark.Rd:40: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
    netbenchmark.data                       html  
    noise.bench                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSkTgKf/R.INSTALL10fc2338383b/netbenchmark/man/noise.bench.Rd:46: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
    ntb_globals                             html  
    pcit.wrap                               html  
    rate                                    html  
    zsc                                     html  
    zscore.wrap                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'netbenchmark' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c netbenchmark_init.c -o netbenchmark_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rate.cpp -o rate.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/netbenchmark.buildbin-libdir/netbenchmark/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'netbenchmark' as netbenchmark_1.16.0.zip
* DONE (netbenchmark)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'netbenchmark' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Wed Oct 16 05:37:51 2019 
*********************************************** 
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 
   1.78    0.17    2.03 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Wed Oct 16 05:37:54 2019 
*********************************************** 
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 
   2.67    0.10    2.76