BioC 3.1: CHECK report for eisa on moscato2
This page was generated on 2015-06-09 09:13:47 -0700 (Tue, 09 Jun 2015).
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 | |
Summary
| Package: eisa
|
| Version: 1.20.0
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| Command: rm -rf eisa.buildbin-libdir eisa.Rcheck && mkdir eisa.buildbin-libdir eisa.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.20.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.20.0.tar.gz
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| StartedAt: 2015-06-09 01:37:37 -0700 (Tue, 09 Jun 2015)
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| EndedAt: 2015-06-09 01:45:57 -0700 (Tue, 09 Jun 2015)
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| EllapsedTime: 499.5 seconds
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| RetCode: 0
|
| 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.20.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.20.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/eisa.Rcheck'
* using R version 3.2.0 (2015-04-16)
* 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 '1.20.0'
* 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 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 '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [155s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 24.14 0.43 24.57
ISA.html 18.48 1.10 20.19
ISA.sweep 14.65 0.42 15.09
ISA.GO 8.89 0.24 16.68
ListHyperGResult-class 8.94 0.18 9.13
ISA.iterate 7.41 0.15 7.58
ISA.unique 7.31 0.18 7.49
gograph 6.84 0.17 7.01
ListHyperGParams-class 6.07 0.13 6.19
ISA.normalize 5.23 0.12 5.35
** running examples for arch 'x64' ... [122s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ISA 20.61 0.53 21.15
ISA.html 17.10 1.03 18.22
ISA.sweep 10.64 0.15 10.80
ISA.GO 6.72 0.23 6.96
gograph 6.56 0.09 6.66
ListHyperGResult-class 6.27 0.10 6.38
ISA.iterate 5.59 0.10 5.67
ListHyperGParams-class 5.35 0.18 5.63
ISA.unique 5.32 0.16 5.47
* 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
'E:/biocbld/bbs-3.1-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_1.20.0.zip
* DONE (eisa)
eisa.Rcheck/examples_i386/eisa-Ex.timings:
| name | user | system | elapsed
|
| ALLModules | 0.22 | 0.00 | 0.21 |
|
| ISA.CHR | 0.64 | 0.01 | 0.65 |
|
| ISA.GO | 8.89 | 0.24 | 16.68 |
|
| ISA.KEGG | 2.80 | 0.03 | 3.02 |
|
| ISA | 24.14 | 0.43 | 24.57 |
|
| ISA.html | 18.48 | 1.10 | 20.19 |
|
| ISA.iterate | 7.41 | 0.15 | 7.58 |
|
| ISA.miRNA | 1.23 | 0.05 | 2.35 |
|
| ISA.normalize | 5.23 | 0.12 | 5.35 |
|
| ISA.sweep | 14.65 | 0.42 | 15.09 |
|
| ISA.unique | 7.31 | 0.18 | 7.49 |
|
| ISA2heatmap | 1.66 | 0.04 | 1.70 |
|
| ISAExpressionSet | 4.27 | 0.11 | 4.38 |
|
| ISAModules-class | 0 | 0 | 0 |
|
| ListHyperGParams-class | 6.07 | 0.13 | 6.19 |
|
| ListHyperGResult-class | 8.94 | 0.18 | 9.13 |
|
| cond.plot | 2.01 | 0.05 | 2.06 |
|
| eisa.biclust | 3.71 | 0.08 | 4.85 |
|
| enrichment | 0.55 | 0.00 | 0.54 |
|
| exp.plot | 1.74 | 0.03 | 1.78 |
|
| gograph | 6.84 | 0.17 | 7.01 |
|
| mnplot | 1.97 | 0.06 | 2.03 |
|
| overlap | 0.51 | 0.22 | 0.73 |
|
| profilePlot | 1.49 | 0.06 | 1.55 |
|
| robustness | 2.41 | 0.10 | 2.51 |
|
eisa.Rcheck/examples_x64/eisa-Ex.timings:
| name | user | system | elapsed
|
| ALLModules | 0.03 | 0.00 | 0.03 |
|
| ISA.CHR | 0.97 | 0.03 | 1.00 |
|
| ISA.GO | 6.72 | 0.23 | 6.96 |
|
| ISA.KEGG | 2.16 | 0.03 | 2.18 |
|
| ISA | 20.61 | 0.53 | 21.15 |
|
| ISA.html | 17.10 | 1.03 | 18.22 |
|
| ISA.iterate | 5.59 | 0.10 | 5.67 |
|
| ISA.miRNA | 0.79 | 0.03 | 0.83 |
|
| ISA.normalize | 4.05 | 0.08 | 4.13 |
|
| ISA.sweep | 10.64 | 0.15 | 10.80 |
|
| ISA.unique | 5.32 | 0.16 | 5.47 |
|
| ISA2heatmap | 1.25 | 0.03 | 1.28 |
|
| ISAExpressionSet | 3.93 | 0.09 | 4.03 |
|
| ISAModules-class | 0.02 | 0.00 | 0.01 |
|
| ListHyperGParams-class | 5.35 | 0.18 | 5.63 |
|
| ListHyperGResult-class | 6.27 | 0.10 | 6.38 |
|
| cond.plot | 1.70 | 0.04 | 1.73 |
|
| eisa.biclust | 3.46 | 0.14 | 3.84 |
|
| enrichment | 0.47 | 0.00 | 0.47 |
|
| exp.plot | 2.06 | 0.03 | 2.09 |
|
| gograph | 6.56 | 0.09 | 6.66 |
|
| mnplot | 1.84 | 0.05 | 1.89 |
|
| overlap | 0.53 | 0.17 | 0.81 |
|
| profilePlot | 1.37 | 0.05 | 1.42 |
|
| robustness | 2.34 | 0.00 | 2.34 |
|