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BioC 3.5: CHECK report for GeneNetworkBuilder on toluca2

This page was generated on 2017-04-23 14:36:43 -0400 (Sun, 23 Apr 2017).

Package 515/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.17.5
Jianhong Ou
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneNetworkBuilder
Last Changed Rev: 125600 / Revision: 129046
Last Changed Date: 2017-01-03 16:14:09 -0500 (Tue, 03 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneNetworkBuilder
Version: 1.17.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneNetworkBuilder_1.17.5.tar.gz
StartedAt: 2017-04-23 04:18:05 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:19:15 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 69.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneNetworkBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneNetworkBuilder_1.17.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneNetworkBuilder.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneNetworkBuilder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneNetworkBuilder’ version ‘1.17.5’
* 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 ‘GeneNetworkBuilder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data          2.8Mb
    doc           5.9Mb
    htmlwidgets   1.8Mb
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘checkCName’ ‘checkMCName’ ‘checkMap’ ‘getMax’ ‘getMedian’ ‘getMin’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
browseNetwork: no visible global function definition for ‘is’
browseNetwork: no visible global function definition for
  ‘getPackageName’
getMedian: no visible global function definition for ‘median’
polishNetwork: no visible global function definition for
  ‘colorRampPalette’
polishNetwork: no visible global function definition for ‘new’
uniqueExprsData: no visible binding for global variable ‘symbols’
Undefined global functions or variables:
  colorRampPalette getPackageName is median new symbols
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "symbols")
  importFrom("methods", "getPackageName", "is", "new")
  importFrom("stats", "median")
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneNetworkBuilder.Rcheck/00check.log’
for details.


GeneNetworkBuilder.Rcheck/00install.out:

* installing *source* package ‘GeneNetworkBuilder’ ...
** 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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c geneTree.cpp -o geneTree.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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c nodefilter.cpp -o nodefilter.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 GeneNetworkBuilder.so geneTree.o nodefilter.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/GeneNetworkBuilder.Rcheck/GeneNetworkBuilder/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneNetworkBuilder)

GeneNetworkBuilder.Rcheck/GeneNetworkBuilder-Ex.timings:

nameusersystemelapsed
browseNetwork3.6380.1513.818
buildNetwork0.3040.0350.348
ce.IDsMap0.5260.0150.551
ce.interactionmap0.0430.0060.048
ce.mapIDs0.4200.0090.436
ce.miRNA.map0.0040.0010.005
convertID0.6600.0200.693
example.data0.0500.0020.053
exportNetwork3.9140.1774.166
filterNetwork1.8280.0731.931
hs.IDsMap0.1350.0020.139
hs.interactionmap0.0380.0040.042
hs.mapIDs0.0540.0010.055
hs.miRNA.map0.0050.0010.005
polishNetwork1.9390.0742.066
uniqueExprsData0.4860.0070.509