BioC 3.3: CHECK report for eisa on windows2.bioconductor.org
This page was generated on 2015-10-27 12:14:35 -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
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| Command: rm -rf eisa.buildbin-libdir eisa.Rcheck && mkdir eisa.buildbin-libdir eisa.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.23.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.23.0.tar.gz
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| StartedAt: 2015-10-27 02:12:00 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 02:17:02 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 301.9 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: eisa.Rcheck
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| Warnings: 0
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Command output
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### Running command:
###
### rm -rf eisa.buildbin-libdir eisa.Rcheck && mkdir eisa.buildbin-libdir eisa.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.23.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.23.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/eisa.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [79s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 13.36 0.71 14.08
ISA.sweep 7.44 0.12 7.56
ISA.GO 5.71 0.11 5.83
gograph 5.13 0.22 5.34
ListHyperGResult-class 5.00 0.19 5.19
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 13.55 0.53 14.08
ISA.sweep 7.58 0.14 7.72
ISA.GO 6.28 0.23 6.51
ListHyperGParams-class 5.24 0.19 5.42
gograph 5.06 0.14 5.20
* 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
'c:/biocbld/bbs-3.3-bioc/meat/eisa.Rcheck/00check.log'
for details.
eisa.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'eisa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eisa' as eisa_1.23.0.zip
* DONE (eisa)
eisa.Rcheck/examples_i386/eisa-Ex.timings:
| name | user | system | elapsed
|
| ALLModules | 0.05 | 0.00 | 0.04 |
|
| ISA.CHR | 1.05 | 0.04 | 1.08 |
|
| ISA.GO | 5.71 | 0.11 | 5.83 |
|
| ISA.KEGG | 1.96 | 0.00 | 1.95 |
|
| ISA | 13.36 | 0.71 | 14.08 |
|
| ISA.html | 0 | 0 | 0 |
|
| ISA.iterate | 4.29 | 0.21 | 4.50 |
|
| ISA.miRNA | 0.50 | 0.00 | 1.91 |
|
| ISA.normalize | 2.60 | 0.08 | 2.67 |
|
| ISA.sweep | 7.44 | 0.12 | 7.56 |
|
| ISA.unique | 3.88 | 0.03 | 3.90 |
|
| ISA2heatmap | 1.14 | 0.00 | 1.14 |
|
| ISAExpressionSet | 3.43 | 0.05 | 3.50 |
|
| ISAModules-class | 0 | 0 | 0 |
|
| ListHyperGParams-class | 4.20 | 0.25 | 4.45 |
|
| ListHyperGResult-class | 5.00 | 0.19 | 5.19 |
|
| cond.plot | 1.56 | 0.03 | 1.59 |
|
| eisa.biclust | 2.84 | 0.12 | 2.98 |
|
| enrichment | 0.3 | 0.0 | 0.3 |
|
| exp.plot | 1.42 | 0.06 | 1.49 |
|
| gograph | 5.13 | 0.22 | 5.34 |
|
| mnplot | 1.76 | 0.08 | 1.84 |
|
| overlap | 0.38 | 0.25 | 0.63 |
|
| profilePlot | 1.17 | 0.02 | 1.19 |
|
| robustness | 2.05 | 0.03 | 2.07 |
|
eisa.Rcheck/examples_x64/eisa-Ex.timings:
| name | user | system | elapsed
|
| ALLModules | 0.27 | 0.00 | 0.27 |
|
| ISA.CHR | 0.81 | 0.02 | 0.83 |
|
| ISA.GO | 6.28 | 0.23 | 6.51 |
|
| ISA.KEGG | 2.25 | 0.03 | 2.28 |
|
| ISA | 13.55 | 0.53 | 14.08 |
|
| ISA.html | 0 | 0 | 0 |
|
| ISA.iterate | 4.19 | 0.16 | 4.34 |
|
| ISA.miRNA | 0.62 | 0.03 | 0.66 |
|
| ISA.normalize | 3.25 | 0.14 | 3.39 |
|
| ISA.sweep | 7.58 | 0.14 | 7.72 |
|
| ISA.unique | 3.64 | 0.16 | 3.80 |
|
| ISA2heatmap | 1.08 | 0.06 | 1.14 |
|
| ISAExpressionSet | 2.97 | 0.06 | 3.03 |
|
| ISAModules-class | 0.01 | 0.00 | 0.02 |
|
| ListHyperGParams-class | 5.24 | 0.19 | 5.42 |
|
| ListHyperGResult-class | 4.70 | 0.11 | 4.81 |
|
| cond.plot | 1.56 | 0.03 | 1.59 |
|
| eisa.biclust | 2.55 | 0.08 | 2.63 |
|
| enrichment | 0.5 | 0.0 | 0.5 |
|
| exp.plot | 1.69 | 0.03 | 1.72 |
|
| gograph | 5.06 | 0.14 | 5.20 |
|
| mnplot | 1.45 | 0.02 | 1.47 |
|
| overlap | 0.38 | 0.31 | 0.69 |
|
| profilePlot | 1.04 | 0.03 | 1.07 |
|
| robustness | 2.21 | 0.10 | 2.30 |
|