BioC 3.4: CHECK report for gCMAP on moscato1

Package: gCMAP

Version: 1.17.0

Command: rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.17.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.17.0.tar.gz

StartedAt: 2016-06-03 04:20:11 -0700 (Fri, 03 Jun 2016)

EndedAt: 2016-06-03 04:27:59 -0700 (Fri, 03 Jun 2016)

EllapsedTime: 468.5 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf gCMAP.buildbin-libdir gCMAP.Rcheck && mkdir gCMAP.buildbin-libdir gCMAP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gCMAP.buildbin-libdir gCMAP_1.17.0.tar.gz >gCMAP.Rcheck\00install.out 2>&1 && cp gCMAP.Rcheck\00install.out gCMAP-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gCMAP.buildbin-libdir --install="check:gCMAP-install.out" --force-multiarch --no-vignettes --timings gCMAP_1.17.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/gCMAP.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gCMAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCMAP' version '1.17.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'bigmemory' '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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  26.54   0.27   29.73
romer_score-methods  8.83   0.01    9.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
mgsa_score-methods  25.64   0.35   26.16
romer_score-methods  7.93   0.00    7.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/gCMAP.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'gCMAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gCMAP' as gCMAP_1.17.0.zip
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.32	0.02	0.33
CMAPResults-class	1.96	0.01	2.09
KEGG2cmap	0	0	0
SignedGeneSet-class	0.05	0.00	0.05
annotate_eset_list	0.11	0.00	0.17
camera_score-methods	0.64	0.00	0.64
center_eSet	0.04	0.00	0.05
connectivity_score-methods	0.16	0.00	1.31
eSetOnDisk	0.02	0.00	0.01
eset_instances	0.06	0.00	0.06
featureScores-methods	0.08	0.00	0.08
fisher_score-methods	0.12	0.00	0.12
gCMAPData-dataset	0.06	0.00	0.07
geneIndex-methods	0.05	0.00	0.04
generate_gCMAP_NChannelSet	0.14	0.01	0.16
gsealm_jg_score-methods	0.23	0.00	0.23
gsealm_score-methods	2.48	0.00	2.48
induceCMAPCollection-methods	0.08	0.00	0.08
mapNmerge	0.02	0.00	0.02
memorize	0	0	0
mergeCMAPs	0.09	0.00	0.09
mgsa_score-methods	26.54	0.27	29.73
minSetSize-methods	0.06	0.00	0.06
mroast_score-methods	0.78	0.02	0.80
romer_score-methods	8.83	0.01	9.05
signedRankSumTest	0	0	0
splitPerturbations	0.10	0.00	0.11
wilcox_score-methods	0.25	0.02	0.27

name	user	system	elapsed
CMAPCollection-class	0.64	0.00	0.64
CMAPResults-class	3.82	0.00	3.82
KEGG2cmap	0	0	0
SignedGeneSet-class	0.11	0.00	0.11
annotate_eset_list	0.25	0.00	0.25
camera_score-methods	1.00	0.01	1.02
center_eSet	0.05	0.00	0.04
connectivity_score-methods	0.22	0.02	0.24
eSetOnDisk	0.01	0.00	0.01
eset_instances	0.11	0.00	0.11
featureScores-methods	0.14	0.01	0.16
fisher_score-methods	0.26	0.00	0.26
gCMAPData-dataset	0.06	0.02	0.08
geneIndex-methods	0.07	0.01	0.08
generate_gCMAP_NChannelSet	0.21	0.00	0.21
gsealm_jg_score-methods	0.35	0.00	0.35
gsealm_score-methods	3.65	0.02	3.66
induceCMAPCollection-methods	0.06	0.02	0.08
mapNmerge	0	0	0
memorize	0	0	0
mergeCMAPs	0.17	0.00	0.17
mgsa_score-methods	25.64	0.35	26.16
minSetSize-methods	0.10	0.02	0.11
mroast_score-methods	1.21	0.05	1.26
romer_score-methods	7.93	0.00	7.93
signedRankSumTest	0.02	0.00	0.01
splitPerturbations	0.10	0.00	0.11
wilcox_score-methods	0.19	0.00	0.19