BioC 3.1: CHECK report for eisa on petty

Package: eisa

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch eisa_1.20.0.tar.gz

StartedAt: 2015-06-08 23:02:55 -0700 (Mon, 08 Jun 2015)

EndedAt: 2015-06-08 23:10:46 -0700 (Mon, 08 Jun 2015)

EllapsedTime: 471.2 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 --no-vignettes --timings --no-multiarch eisa_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/eisa.Rcheck’
* using R version 3.2.0 Patched (2015-04-19 r68206)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.20.0’
* 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 ... [25s/25s] 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:
  ‘biclust’ ‘GO.db’ ‘igraph’ ‘KEGG.db’ ‘MASS’ ‘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
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 ‘subgraph’
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’
gographPlot: no visible global function definition for ‘V’
html.df: no visible global function definition for ‘xtable’
isa.autogen.module : tabulate: no visible binding for global variable
  ‘KEGGPATHID2NAME’
isa.autogen.module : gp: no visible global function definition for
  ‘graph.empty’
isa.autogen.module : ann: no visible global function definition for
  ‘vcount’
isa.autogen.module : ann: no visible global function definition for ‘V’
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’
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’
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’
htmlReport,GOListHyperGResult: no visible binding for global variable
  ‘GOTERM’
htmlReport,KEGGListHyperGResult: no visible binding for global variable
  ‘KEGGPATHID2NAME’
* 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 ... [210s/213s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA.html               32.570  2.285  36.100
ISA                    31.583  0.956  32.640
ISA.sweep              16.298  1.834  18.180
gograph                11.788  0.635  12.754
ISA.GO                 11.705  0.488  12.473
ListHyperGResult-class 11.137  0.583  11.745
ISA.iterate             8.912  1.003   9.929
ListHyperGParams-class  9.325  0.504  10.511
ISA.unique              8.748  0.748   9.511
ISA.normalize           6.936  0.427   7.378
eisa.biclust            5.765  1.162   6.958
ISAExpressionSet        6.352  0.388   6.761
* 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-3.1-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	0.029	0.003	0.032
ISA.CHR	1.270	0.060	1.415
ISA.GO	11.705	0.488	12.473
ISA.KEGG	3.791	0.073	3.902
ISA	31.583	0.956	32.640
ISA.html	32.570	2.285	36.100
ISA.iterate	8.912	1.003	9.929
ISA.miRNA	1.618	0.090	1.831
ISA.normalize	6.936	0.427	7.378
ISA.sweep	16.298	1.834	18.180
ISA.unique	8.748	0.748	9.511
ISA2heatmap	1.750	0.118	1.874
ISAExpressionSet	6.352	0.388	6.761
ISAModules-class	0.019	0.002	0.021
ListHyperGParams-class	9.325	0.504	10.511
ListHyperGResult-class	11.137	0.583	11.745
cond.plot	2.402	0.180	2.631
eisa.biclust	5.765	1.162	6.958
enrichment	0.889	0.025	0.938
exp.plot	2.488	0.233	2.729
gograph	11.788	0.635	12.754
mnplot	2.940	0.201	3.146
overlap	0.996	1.094	2.122
profilePlot	1.741	0.091	1.837
robustness	3.503	0.233	3.742