BioC 3.3: CHECK report for gCMAP on oaxaca

Package: gCMAP

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gCMAP_1.16.0.tar.gz

StartedAt: 2016-06-07 01:58:01 -0700 (Tue, 07 Jun 2016)

EndedAt: 2016-06-07 02:03:40 -0700 (Tue, 07 Jun 2016)

EllapsedTime: 339.5 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck’
* using R version 3.3.0 (2016-05-03)
* 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 ‘1.16.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  16.032  0.699 105.240
romer_score-methods  6.598  0.742   6.697
* 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-3.3-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	1.084	0.351	1.186
CMAPResults-class	2.457	0.096	2.565
KEGG2cmap	0.000	0.000	0.001
SignedGeneSet-class	0.065	0.003	0.068
annotate_eset_list	0.116	0.008	0.164
camera_score-methods	0.555	0.101	1.104
center_eSet	0.034	0.004	0.037
connectivity_score-methods	1.585	0.760	0.929
eSetOnDisk	0.008	0.001	0.009
eset_instances	0.075	0.012	0.087
featureScores-methods	0.183	0.079	0.786
fisher_score-methods	1.688	0.840	0.825
gCMAPData-dataset	0.182	0.086	0.723
geneIndex-methods	0.808	0.408	0.588
generate_gCMAP_NChannelSet	0.194	0.023	0.218
gsealm_jg_score-methods	1.685	0.768	0.916
gsealm_score-methods	3.114	0.125	3.700
induceCMAPCollection-methods	0.768	0.338	0.562
mapNmerge	0.001	0.000	0.001
memorize	0.009	0.001	0.010
mergeCMAPs	0.106	0.018	0.124
mgsa_score-methods	16.032	0.699	105.240
minSetSize-methods	0.808	0.403	0.761
mroast_score-methods	1.627	0.541	1.496
romer_score-methods	6.598	0.742	6.697
signedRankSumTest	0.002	0.000	0.002
splitPerturbations	0.078	0.004	0.082
wilcox_score-methods	1.534	0.735	0.857