Package: eisa

Version: 1.30.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.30.0.tar.gz

StartedAt: 2018-04-11 23:10:42 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:13:55 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 192.1 seconds

RetCode: 0

Status:  OK

CheckDir: eisa.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/eisa.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.30.0’
* 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 ‘eisa’ 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’ ‘MASS’ ‘biclust’ ‘igraph’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘Category:::getDataEnv’ ‘Category:::getKeggToProbeMap’
  ‘Category:::probeToEntrezMapHelper’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ISA : <anonymous>: no visible global function definition for ‘IQR’
ISA: no visible binding for global variable ‘var’
ISA2heatmap: no visible global function definition for ‘heatmap’
ISACHR: no visible global function definition for ‘p.adjust’
ISAEnrichment: no visible global function definition for ‘p.adjust’
ISAGO: no visible global function definition for ‘p.adjust’
ISAHTMLModules: no visible global function definition for ‘GO_dbconn’
ISAHTMLModules : go.graph: no visible global function definition for
  ‘graph.data.frame’
ISAHTMLTable: no visible global function definition for ‘GO_dbconn’
ISAHTMLTable : f: no visible binding for global variable
  ‘KEGGPATHID2NAME’
ISAKEGG: no visible global function definition for ‘p.adjust’
ISASweepGraph: no visible global function definition for ‘V’
ISASweepGraph: no visible global function definition for ‘V<-’
ISASweepGraph: no visible global function definition for
  ‘remove.vertex.attribute’
ISASweepGraphPlot: no visible global function definition for ‘V’
ISASweepGraphPlot: no visible global function definition for ‘axis’
ISASweepGraphPlot: no visible global function definition for ‘par’
ISASweepGraphPlot: no visible global function definition for ‘abline’
ISASweepGraphPlot: no visible global function definition for ‘text’
ISAmiRNA: no visible global function definition for ‘p.adjust’
cnvrt.coords: no visible global function definition for ‘xy.coords’
cnvrt.coords: no visible global function definition for ‘par’
condPlot: no visible global function definition for ‘sd’
condPlot: no visible global function definition for ‘par’
condPlot: no visible global function definition for ‘barplot’
condPlot: no visible global function definition for ‘abline’
condPlot: no visible global function definition for ‘text’
condPlot: no visible global function definition for ‘points’
convert.miRNA: no visible global function definition for ‘read.delim’
expPlot: no visible global function definition for ‘layout’
expPlot: no visible global function definition for ‘par’
expPlot: no visible global function definition for ‘image’
expPlot: no visible global function definition for ‘title’
expPlot: no visible global function definition for ‘axis’
expPlot: no visible global function definition for ‘abline’
expPlot: no visible global function definition for ‘lines’
expPlot: no visible global function definition for ‘text’
expPlot: no visible global function definition for ‘segments’
expPlotColbar: no visible global function definition for ‘par’
expPlotColbar: no visible global function definition for ‘image’
expPlotColbar: no visible global function definition for ‘axis’
expPlotColbar: no visible global function definition for ‘abline’
expPlotCreate: no visible global function definition for ‘hcl’
gograph: no visible binding for global variable ‘GOTERM’
gograph: no visible global function definition for ‘GO_dbconn’
gograph: no visible global function definition for ‘graph.data.frame’
gograph: no visible global function definition for ‘V’
gograph: no visible global function definition for ‘vcount’
gograph: no visible global function definition for ‘neighborhood’
gograph: no visible global function definition for ‘induced_subgraph’
gograph: no visible global function definition for ‘hcl’
gograph: no visible global function definition for ‘V<-’
gograph: no visible global function definition for ‘topological.sort’
gograph: no visible global function definition for ‘unfold.tree’
gograph: no visible global function definition for ‘E’
gograph: no visible global function definition for ‘E<-’
gograph: no visible global function definition for
  ‘layout.reingold.tilford’
gograph: no visible global function definition for ‘as_ids’
gographPlot: no visible global function definition for ‘dev.cur’
gographPlot: no visible global function definition for ‘par’
gographPlot: no visible global function definition for ‘V’
gographPlot: no visible global function definition for ‘text’
html.df: no visible global function definition for ‘xtable’
isa.autogen.module : tabulate: no visible binding for global variable
  ‘KEGGPATHID2NAME’
isa.autogen.module: no visible global function definition for ‘png’
isa.autogen.module: no visible global function definition for ‘dev.off’
isa.autogen.module : gp: no visible global function definition for
  ‘graph.empty’
isa.autogen.module : gp: no visible global function definition for
  ‘png’
isa.autogen.module : gp: no visible global function definition for
  ‘dev.off’
isa.autogen.module : ann: no visible global function definition for
  ‘vcount’
isa.autogen.module : ann: no visible global function definition for ‘V’
mnplot: no visible global function definition for ‘abline’
overlap: no visible global function definition for ‘cor’
overlap: no visible global function definition for ‘isoMDS’
overlap: no visible global function definition for ‘graph.adjacency’
overlap: no visible global function definition for ‘V’
overlap: no visible global function definition for ‘V<-’
overlap: no visible global function definition for ‘graph.empty’
overlap: no visible global function definition for ‘E’
overlap: no visible global function definition for ‘E<-’
overlap: no visible global function definition for
  ‘layout.fruchterman.reingold’
overlap: no visible global function definition for ‘layout.drl’
overlap: no visible global function definition for ‘ecount’
overlapPlot: no visible global function definition for ‘V’
overlapPlot: no visible global function definition for ‘layout.norm’
overlapPlot: no visible global function definition for ‘par’
profilePlot: no visible global function definition for ‘gray’
profilePlot : pp: no visible global function definition for ‘par’
profilePlot : pp: no visible global function definition for ‘title’
profilePlot : pp: no visible global function definition for ‘axis’
profilePlot : pp: no visible global function definition for ‘lines’
profilePlot: no visible global function definition for ‘par’
getFeatureMatrix,ISAModules: no visible global function definition for
  ‘Matrix’
getSampleMatrix,ISAModules: no visible global function definition for
  ‘Matrix’
htmlReport,GOListHyperGResult: no visible binding for global variable
  ‘GOTERM’
htmlReport,KEGGListHyperGResult: no visible binding for global variable
  ‘KEGGPATHID2NAME’
Undefined global functions or variables:
  E E<- GOTERM GO_dbconn IQR KEGGPATHID2NAME Matrix V V<- abline as_ids
  axis barplot cor dev.cur dev.off ecount graph.adjacency
  graph.data.frame graph.empty gray hcl heatmap image induced_subgraph
  isoMDS layout layout.drl layout.fruchterman.reingold layout.norm
  layout.reingold.tilford lines neighborhood p.adjust par png points
  read.delim remove.vertex.attribute sd segments text title
  topological.sort unfold.tree var vcount xtable xy.coords
Consider adding
  importFrom("grDevices", "dev.cur", "dev.off", "gray", "hcl", "png",
             "xy.coords")
  importFrom("graphics", "abline", "axis", "barplot", "image", "layout",
             "lines", "par", "points", "segments", "text", "title")
  importFrom("stats", "IQR", "cor", "heatmap", "p.adjust", "sd", "var")
  importFrom("utils", "read.delim")
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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ISA         16.040  0.088  16.170
ISA.sweep   10.196  0.044  10.264
ISA.unique   6.532  0.040   6.579
ISA.iterate  6.528  0.044   6.573
ISA.GO       4.540  0.108   7.053
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/eisa.Rcheck/00check.log’
for details.

* installing *source* package ‘eisa’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class “Biclust”
in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class “Biclust”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eisa)

name	user	system	elapsed
ALLModules	0.032	0.004	0.040
ISA.CHR	1.572	0.020	1.950
ISA.GO	4.540	0.108	7.053
ISA.KEGG	1.692	0.004	1.734
ISA	16.040	0.088	16.170
ISA.html	0.000	0.000	0.001
ISA.iterate	6.528	0.044	6.573
ISA.miRNA	0.816	0.012	0.885
ISA.normalize	3.140	0.048	3.189
ISA.sweep	10.196	0.044	10.264
ISA.unique	6.532	0.040	6.579
ISA2heatmap	1.080	0.012	1.092
ISAExpressionSet	2.776	0.064	2.843
ISAModules-class	0.008	0.000	0.009
ListHyperGParams-class	2.944	0.032	2.978
ListHyperGResult-class	3.564	0.052	3.621
cond.plot	1.296	0.028	1.324
eisa.biclust	2.668	0.036	2.965
enrichment	0.320	0.004	0.324
exp.plot	1.352	0.044	1.399
gograph	4.504	0.064	4.576
mnplot	1.672	0.032	1.707
overlap	0.312	0.192	0.504
profilePlot	1.152	0.044	1.198
robustness	1.784	0.008	1.795