eisa 1.20.0
Gabor Csardi
| Snapshot Date: 2015-06-08 17:20:17 -0700 (Mon, 08 Jun 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/eisa | | Last Changed Rev: 102591 / Revision: 104704 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/eisa.Rcheck’
* using R version 3.2.0 (2015-04-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.20.0’
* 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 ... [11s/12s] 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 ‘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’
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 ... [97s/97s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 16.579 0.036 16.689
ISA.html 13.464 0.207 13.745
ISA.sweep 9.147 0.000 9.187
ISA.GO 5.526 0.100 5.654
gograph 5.279 0.088 5.369
* 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-3.1-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)