BioC 3.3: CHECK report for gCMAP on morelia

Package: gCMAP

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz

StartedAt: 2016-04-21 02:42:53 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 02:48:07 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 314.7 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCMAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCMAP’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘bigmemoryExtras’
* 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 ‘gCMAP’ can be installed ... [30s/33s] 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
  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
.jg: no visible global function definition for ‘na.omit’
.jg: no visible global function definition for ‘pnorm’
.overview.density: no visible global function definition for ‘density’
.overview.density: no visible global function definition for ‘polygon’
.overview.density: no visible global function definition for ‘lines’
.overview.density: no visible global function definition for ‘dnorm’
.overview.density: no visible global function definition for ‘rug’
.overview.density: no visible global function definition for ‘legend’
.overview.heatmap: no visible global function definition for
  ‘colorRampPalette’
.overview.heatmap: no visible global function definition for ‘image’
.signed.incidence : <anonymous>: no visible global function definition
  for ‘na.omit’
center.function: no visible global function definition for ‘median’
center.function: no visible global function definition for ‘density’
center_eSet : center.function: no visible global function definition
  for ‘median’
center_eSet : center.function: no visible global function definition
  for ‘density’
center_eSet : mad.about.mode: no visible global function definition for
  ‘median’
eSetProbeToGene: no visible global function definition for ‘na.omit’
eSetProbeToGene : <anonymous>: no visible global function definition
  for ‘ave’
fisher_p : <anonymous>: no visible global function definition for
  ‘dhyper’
mapNmerge: no visible global function definition for ‘na.omit’
mapNmerge : <anonymous> : <anonymous>: no visible global function
  definition for ‘ave’
pairwise_DESeq: no visible global function definition for
  ‘model.matrix’
pairwise_compare_limma: no visible global function definition for
  ‘model.matrix’
signedRankSumTest: no visible global function definition for ‘pt’
wiki2cmap: no visible global function definition for ‘URLencode’
wiki2cmap: no visible global function definition for ‘download.file’
wiki2cmap: no visible global function definition for ‘unzip’
wiki2cmap: no visible binding for global variable ‘read.delim’
wiki2cmap : <anonymous>: no visible global function definition for
  ‘na.omit’
zScores: no visible global function definition for ‘qnorm’
camera_score,eSet-CMAPCollection: no visible global function definition
  for ‘camera’
connectivity_score,eSet-CMAPCollection: no visible global function
  definition for ‘na.omit’
effect<-,CMAPResults: no visible global function definition for
  ‘update’
fisher_score,CMAPCollection-CMAPCollection-character : <anonymous>: no
  visible global function definition for ‘p.adjust’
gsealm_jg_score,CMAPCollection-eSet : <anonymous>: no visible global
  function definition for ‘p.adjust’
gsealm_jg_score,matrix_or_big.matrix-CMAPCollection : <anonymous>: no
  visible global function definition for ‘p.adjust’
gsealm_score,ExpressionSet-CMAPCollection: no visible global function
  definition for ‘as.formula’
gsealm_score,ExpressionSet-CMAPCollection: no visible binding for
  global variable ‘pnorm’
gsealm_score,ExpressionSet-CMAPCollection: no visible global function
  definition for ‘p.adjust’
induceCMAPCollection,eSet : <anonymous>: no visible global function
  definition for ‘mwhich’
mroast_score,eSet-CMAPCollection: no visible global function definition
  for ‘mroast’
nFound<-,CMAPResults: no visible global function definition for
  ‘update’
nSet<-,CMAPResults: no visible global function definition for ‘update’
padj<-,CMAPResults: no visible global function definition for ‘update’
plot,CMAPResults-ANY: no visible global function definition for
  ‘plot.new’
plot,CMAPResults-ANY: no visible global function definition for ‘par’
romer_score,eSet-CMAPCollection: no visible global function definition
  for ‘romer’
romer_score,eSet-CMAPCollection: no visible global function definition
  for ‘p.adjust’
set<-,CMAPResults: no visible global function definition for ‘update’
wilcox_score,CMAPCollection-eSet: no visible global function definition
  for ‘na.omit’
wilcox_score,CMAPCollection-eSet : <anonymous>: no visible global
  function definition for ‘p.adjust’
wilcox_score,matrix-CMAPCollection: no visible global function
  definition for ‘na.omit’
wilcox_score,matrix-CMAPCollection : <anonymous>: no visible global
  function definition for ‘p.adjust’
Undefined global functions or variables:
  URLencode as.formula ave camera colorRampPalette density dhyper dnorm
  download.file image legend lines median model.matrix mroast mwhich
  na.omit p.adjust par plot.new pnorm polygon pt qnorm read.delim romer
  rug unzip update
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "image", "legend", "lines", "par", "plot.new",
             "polygon", "rug")
  importFrom("stats", "as.formula", "ave", "density", "dhyper", "dnorm",
             "median", "model.matrix", "na.omit", "p.adjust", "pnorm",
             "pt", "qnorm", "update")
  importFrom("utils", "URLencode", "download.file", "read.delim",
             "unzip")
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 ... [64s/68s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  18.668  0.548  30.426
romer_score-methods  7.707  0.753   8.100
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [42s/38s]
 [42s/38s] 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-3.3-bioc/meat/gCMAP.Rcheck/00check.log’
for details.

* installing *source* package ‘gCMAP’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	1.253	0.396	1.255
CMAPResults-class	2.630	0.112	2.847
KEGG2cmap	0.001	0.001	0.001
SignedGeneSet-class	0.068	0.004	0.073
annotate_eset_list	0.144	0.008	0.192
camera_score-methods	0.640	0.111	1.352
center_eSet	0.037	0.003	0.040
connectivity_score-methods	1.811	0.857	1.073
eSetOnDisk	0.007	0.000	0.008
eset_instances	0.095	0.015	0.110
featureScores-methods	0.208	0.082	0.867
fisher_score-methods	1.845	0.919	0.951
gCMAPData-dataset	0.201	0.094	0.877
geneIndex-methods	0.941	0.477	0.665
generate_gCMAP_NChannelSet	0.244	0.027	0.272
gsealm_jg_score-methods	1.883	0.826	1.116
gsealm_score-methods	3.532	0.146	4.178
induceCMAPCollection-methods	0.822	0.366	0.635
mapNmerge	0.000	0.000	0.001
memorize	0.009	0.001	0.009
mergeCMAPs	0.114	0.014	0.128
mgsa_score-methods	18.668	0.548	30.426
minSetSize-methods	1.039	0.514	0.856
mroast_score-methods	1.834	0.589	1.865
romer_score-methods	7.707	0.753	8.100
signedRankSumTest	0.003	0.000	0.004
splitPerturbations	0.103	0.006	0.114
wilcox_score-methods	1.787	0.885	1.118