netbenchmark 1.9.0
Pau Bellot
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/netbenchmark | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/netbenchmark.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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 9.927 0.191 10.345
Genie3.wrap 8.662 0.090 9.007
netbenchmark.data 8.453 0.110 8.812
* 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.
* 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)