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BioC 3.2: CHECK report for eisa on oaxaca

This page was generated on 2015-10-27 17:39:05 -0400 (Tue, 27 Oct 2015).

Package 311/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eisa 1.22.0
Gabor Csardi
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/eisa
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: eisa
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings eisa_1.22.0.tar.gz
StartedAt: 2015-10-27 03:18:45 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:23:33 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 288.1 seconds
RetCode: 0
Status:  OK 
CheckDir: eisa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings eisa_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/eisa.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.22.0’
* 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 ... [16s/16s] 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
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’
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 ‘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 ‘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’
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’
getFeatureMatrix,ISAModules : .local: no visible global function
  definition for ‘Matrix’
getSampleMatrix,ISAModules : .local: 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’
* 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 ... [96s/129s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    14.964  0.692  15.737
ISA.sweep              10.165  1.186  11.377
gograph                 7.467  0.458  12.886
ListHyperGResult-class  6.856  0.426   8.752
ISA.GO                  6.870  0.343   9.702
ListHyperGParams-class  5.415  0.307  25.682
* 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-3.2-bioc/meat/eisa.Rcheck/00check.log’
for details.


eisa.Rcheck/00install.out:

* 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)

eisa.Rcheck/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.0120.0010.013
ISA.CHR0.9720.0261.904
ISA.GO6.8700.3439.702
ISA.KEGG2.0110.0382.049
ISA14.964 0.69215.737
ISA.html0.0010.0010.003
ISA.iterate4.4260.3964.826
ISA.miRNA0.8810.0401.495
ISA.normalize3.9020.2634.169
ISA.sweep10.165 1.18611.377
ISA.unique4.3000.4124.713
ISA2heatmap1.0360.0351.072
ISAExpressionSet2.9830.1293.113
ISAModules-class0.0130.0010.024
ListHyperGParams-class 5.415 0.30725.682
ListHyperGResult-class6.8560.4268.752
cond.plot1.5330.1032.545
eisa.biclust2.9570.5693.994
enrichment0.4370.0080.445
exp.plot1.5740.0871.753
gograph 7.467 0.45812.886
mnplot2.0420.1262.175
overlap0.0980.0290.171
profilePlot1.2190.0561.279
robustness2.2390.1162.357