Package: eisa

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.34.0.tar.gz

StartedAt: 2019-04-15 23:43:43 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:47:56 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 252.8 seconds

RetCode: 0

Status:  OK

CheckDir: eisa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/eisa.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.34.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    18.010  0.777  18.993
ISA.sweep              14.127  1.720  15.957
ISA.iterate             7.830  0.502   8.413
ISA.unique              6.669  0.435   7.154
ISA.GO                  6.100  0.343   6.522
gograph                 6.050  0.320   6.438
ListHyperGResult-class  5.416  0.248   5.740
ListHyperGParams-class  4.950  0.251   5.260
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/eisa.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL eisa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘eisa’ ...
** R
** data
** inst
** byte-compile and prepare 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	0.039	0.006	0.045
ISA.CHR	1.163	0.047	1.224
ISA.GO	6.100	0.343	6.522
ISA.KEGG	2.447	0.049	2.518
ISA	18.010	0.777	18.993
ISA.html	0.001	0.000	0.001
ISA.iterate	7.830	0.502	8.413
ISA.miRNA	0.927	0.046	1.035
ISA.normalize	4.530	0.290	4.866
ISA.sweep	14.127	1.720	15.957
ISA.unique	6.669	0.435	7.154
ISA2heatmap	1.015	0.040	1.066
ISAExpressionSet	4.364	0.224	4.647
ISAModules-class	0.012	0.003	0.014
ListHyperGParams-class	4.950	0.251	5.260
ListHyperGResult-class	5.416	0.248	5.740
cond.plot	1.641	0.115	1.775
eisa.biclust	3.833	0.732	4.632
enrichment	0.427	0.007	0.441
exp.plot	1.621	0.109	1.745
gograph	6.050	0.320	6.438
mnplot	2.028	0.126	2.180
overlap	0.086	0.031	0.119
profilePlot	1.194	0.064	1.268
robustness	1.884	0.143	2.063