BioC 3.3: CHECK report for eisa on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:48 -0400 (Tue, 27 Oct 2015).
eisa 1.23.0
Gabor Csardi
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/eisa | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
Summary
| Package: eisa |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.23.0.tar.gz |
| StartedAt: 2015-10-27 03:35:41 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:39:03 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 201.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: eisa.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/eisa.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.23.0’
* 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 ... [10s/10s] 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: 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 KEGGPATHID2NAME Matrix V V<- as_ids ecount
graph.adjacency graph.data.frame graph.empty induced_subgraph isoMDS
layout.drl layout.fruchterman.reingold layout.norm
layout.reingold.tilford neighborhood remove.vertex.attribute
topological.sort unfold.tree vcount xtable
* 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 ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 16.938 0.072 17.017
ISA.sweep 8.772 0.020 8.801
gograph 7.540 0.096 7.639
ISA.GO 7.487 0.084 7.599
ListHyperGResult-class 5.817 0.064 5.889
* 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-3.3-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:
| name | user | system | elapsed
|
| ALLModules | 0.037 | 0.004 | 0.041 |
|
| ISA.CHR | 1.106 | 0.012 | 1.119 |
|
| ISA.GO | 7.487 | 0.084 | 7.599 |
|
| ISA.KEGG | 2.309 | 0.020 | 2.329 |
|
| ISA | 16.938 | 0.072 | 17.017 |
|
| ISA.html | 0 | 0 | 0 |
|
| ISA.iterate | 4.582 | 0.008 | 4.592 |
|
| ISA.miRNA | 0.904 | 0.000 | 0.911 |
|
| ISA.normalize | 3.013 | 0.024 | 3.037 |
|
| ISA.sweep | 8.772 | 0.020 | 8.801 |
|
| ISA.unique | 3.753 | 0.016 | 3.774 |
|
| ISA2heatmap | 1.028 | 0.012 | 1.041 |
|
| ISAExpressionSet | 2.822 | 0.012 | 2.836 |
|
| ISAModules-class | 0.009 | 0.000 | 0.008 |
|
| ListHyperGParams-class | 3.803 | 0.032 | 3.839 |
|
| ListHyperGResult-class | 5.817 | 0.064 | 5.889 |
|
| cond.plot | 1.493 | 0.032 | 1.526 |
|
| eisa.biclust | 2.819 | 0.024 | 2.849 |
|
| enrichment | 0.486 | 0.000 | 0.486 |
|
| exp.plot | 1.648 | 0.016 | 1.667 |
|
| gograph | 7.540 | 0.096 | 7.639 |
|
| mnplot | 1.771 | 0.004 | 1.775 |
|
| overlap | 0.369 | 0.168 | 0.537 |
|
| profilePlot | 1.240 | 0.060 | 1.301 |
|
| robustness | 2.008 | 0.004 | 2.015 |
|