GeneAnswers 2.17.0
Lei Huang and Gang Feng
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers | | Last Changed Rev: 123157 / Revision: 129046 | | Last Changed Date: 2016-10-28 13:56:24 -0400 (Fri, 28 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneAnswers_2.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.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 ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’
‘Heatplus’ ‘RColorBrewer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GeneAnswers’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 35.5Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.0Mb
doc 1.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘annotate’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘Biobase’ ‘Heatplus’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘reactome.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GeneAnswers/R/zzz.R’:
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
.catsCluster: no visible global function definition for ‘par’
.catsCluster: no visible global function definition for ‘plot’
.defaultHeatmapColors: no visible global function definition for ‘rgb’
.drawHTMLtable: no visible global function definition for
‘colorRampPalette’
.drawTable: no visible global function definition for ‘par’
.drawTable: no visible global function definition for ‘image’
.drawTable: no visible global function definition for ‘abline’
.drawTable: no visible global function definition for ‘axis’
.drawTable: no visible global function definition for ‘points’
.heatmap.mds: no visible global function definition for
‘colorRampPalette’
.heatmap.mds: no visible global function definition for ‘layout’
.heatmap.mds: no visible global function definition for ‘par’
.heatmap.mds: no visible global function definition for ‘image’
.heatmap.mds: no visible global function definition for ‘axis’
.heatmap.mds: no visible global function definition for ‘box’
buildNet: no visible global function definition for ‘colorRampPalette’
buildNet: no visible global function definition for ‘plot’
chartPlots: no visible global function definition for ‘x11’
chartPlots: no visible global function definition for ‘pie’
chartPlots: no visible global function definition for ‘rainbow’
chartPlots: no visible global function definition for ‘barplot’
drawTable: no visible global function definition for ‘colorRampPalette’
drawTable: no visible global function definition for ‘x11’
drawTable: no visible global function definition for ‘par’
drawTable: no visible global function definition for ‘image’
drawTable: no visible global function definition for ‘abline’
drawTable: no visible global function definition for ‘axis’
drawTable: no visible global function definition for ‘text’
drawTable: no visible global function definition for ‘box’
drawTable: no visible global function definition for ‘dev.set’
drawTable: no visible global function definition for ‘dev.prev’
geneAnnotationHeatmap: no visible global function definition for
‘colorRampPalette’
geneAnnotationHeatmap: no visible global function definition for
‘layout’
geneConceptNet: no visible global function definition for
‘colorRampPalette’
getHomoGeneIDs: no visible global function definition for ‘useMart’
getHomoGeneIDs: no visible global function definition for ‘getLDS’
getTotalGeneNumber: no visible global function definition for
‘count.mappedkeys’
getTotalGeneNumber: no visible global function definition for ‘toTable’
getTotalGeneNumber: no visible binding for global variable
‘reactomePATHNAME2ID’
groupReport: no visible global function definition for ‘png’
groupReport: no visible global function definition for ‘dev.off’
groupReport: no visible global function definition for ‘rgb’
groupReport: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
abline axis barplot box col2rgb colorRampPalette count.mappedkeys
dev.off dev.prev dev.set getLDS image layout par pie plot png points
rainbow reactomePATHNAME2ID rgb text toTable useMart x11
Consider adding
importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
"dev.prev", "dev.set", "png", "rainbow", "rgb", "x11")
importFrom("graphics", "abline", "axis", "barplot", "box", "image",
"layout", "par", "pie", "plot", "points", "text")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... 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
geneAnswersReadable 63.424 3.381 67.672
GeneAnswers-class 36.694 1.971 39.036
getConnectedGraph 33.252 1.616 35.190
geneAnswersSort 33.157 1.647 35.234
GeneAnswers-package 32.848 1.605 34.861
geneAnswersBuilder 32.804 1.574 35.017
getMultiLayerGraphIDs 32.816 1.537 34.713
geneAnswersConceptNet 32.586 1.657 34.901
geneAnswersConcepts 32.468 1.635 34.582
geneAnswersChartPlots 32.312 1.635 34.841
buildNet 32.302 1.562 34.545
geneAnswersHomoMapping 32.265 1.579 34.420
geneAnswersConceptRelation 31.869 1.522 33.777
geneAnswersHeatmap 31.557 1.589 33.517
getGOList 17.642 1.101 18.862
* 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.
* installing *source* package ‘GeneAnswers’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
* DONE (GeneAnswers)