Gabor Csardi
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/eisa |
| Branch: RELEASE_3_11 |
| Last Commit: 5f3dd5e |
| Last Changed Date: 2020-04-27 14:20:46 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:30 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE eisa PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 534/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| eisa 1.40.0 Gabor Csardi
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: eisa |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings eisa_1.40.0.tar.gz |
| StartedAt: 2020-10-17 03:41:00 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:49:06 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 486.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: eisa.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings eisa_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/eisa.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.40.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/mnplot.Rd:36: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/profilePlot.Rd:45: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/profilePlot.Rd:47: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/eisa.Rcheck/00install.out' for details.
* 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
ISA : <anonymous>: no visible global function definition for 'IQR'
ISA: no visible binding for global variable 'var'
ISA2heatmap: no visible global function definition for 'heatmap'
ISACHR: no visible global function definition for 'p.adjust'
ISAEnrichment: no visible global function definition for 'p.adjust'
ISAGO: no visible global function definition for 'p.adjust'
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'
ISAKEGG: no visible global function definition for 'p.adjust'
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'
ISASweepGraphPlot: no visible global function definition for 'axis'
ISASweepGraphPlot: no visible global function definition for 'par'
ISASweepGraphPlot: no visible global function definition for 'abline'
ISASweepGraphPlot: no visible global function definition for 'text'
ISAmiRNA: no visible global function definition for 'p.adjust'
cnvrt.coords: no visible global function definition for 'xy.coords'
cnvrt.coords: no visible global function definition for 'par'
condPlot: no visible global function definition for 'sd'
condPlot: no visible global function definition for 'par'
condPlot: no visible global function definition for 'barplot'
condPlot: no visible global function definition for 'abline'
condPlot: no visible global function definition for 'text'
condPlot: no visible global function definition for 'points'
convert.miRNA: no visible global function definition for 'read.delim'
expPlot: no visible global function definition for 'layout'
expPlot: no visible global function definition for 'par'
expPlot: no visible global function definition for 'image'
expPlot: no visible global function definition for 'title'
expPlot: no visible global function definition for 'axis'
expPlot: no visible global function definition for 'abline'
expPlot: no visible global function definition for 'lines'
expPlot: no visible global function definition for 'text'
expPlot: no visible global function definition for 'segments'
expPlotColbar: no visible global function definition for 'par'
expPlotColbar: no visible global function definition for 'image'
expPlotColbar: no visible global function definition for 'axis'
expPlotColbar: no visible global function definition for 'abline'
expPlotCreate: no visible global function definition for 'hcl'
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 'hcl'
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 'dev.cur'
gographPlot: no visible global function definition for 'par'
gographPlot: no visible global function definition for 'V'
gographPlot: no visible global function definition for 'text'
html.df: no visible global function definition for 'xtable'
isa.autogen.module : tabulate: no visible binding for global variable
'KEGGPATHID2NAME'
isa.autogen.module: no visible global function definition for 'png'
isa.autogen.module: no visible global function definition for 'dev.off'
isa.autogen.module : gp: no visible global function definition for
'graph.empty'
isa.autogen.module : gp: no visible global function definition for
'png'
isa.autogen.module : gp: no visible global function definition for
'dev.off'
isa.autogen.module : ann: no visible global function definition for
'vcount'
isa.autogen.module : ann: no visible global function definition for 'V'
mnplot: no visible global function definition for 'abline'
overlap: no visible global function definition for 'cor'
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'
overlapPlot: no visible global function definition for 'par'
profilePlot: no visible global function definition for 'gray'
profilePlot : pp: no visible global function definition for 'par'
profilePlot : pp: no visible global function definition for 'title'
profilePlot : pp: no visible global function definition for 'axis'
profilePlot : pp: no visible global function definition for 'lines'
profilePlot: no visible global function definition for 'par'
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 IQR KEGGPATHID2NAME Matrix V V<- abline as_ids
axis barplot cor dev.cur dev.off ecount graph.adjacency
graph.data.frame graph.empty gray hcl heatmap image induced_subgraph
isoMDS layout layout.drl layout.fruchterman.reingold layout.norm
layout.reingold.tilford lines neighborhood p.adjust par png points
read.delim remove.vertex.attribute sd segments text title
topological.sort unfold.tree var vcount xtable xy.coords
Consider adding
importFrom("grDevices", "dev.cur", "dev.off", "gray", "hcl", "png",
"xy.coords")
importFrom("graphics", "abline", "axis", "barplot", "image", "layout",
"lines", "par", "points", "segments", "text", "title")
importFrom("stats", "IQR", "cor", "heatmap", "p.adjust", "sd", "var")
importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ISA 15.77 0.56 16.33
ISA.sweep 14.42 0.96 15.39
ISA.iterate 8.85 0.43 9.27
ISA.unique 8.40 0.61 9.02
ListHyperGResult-class 5.77 0.20 5.97
eisa.biclust 5.36 0.48 8.27
ListHyperGParams-class 5.31 0.23 7.85
ISA.GO 4.28 0.22 5.55
ISA.miRNA 0.89 0.07 11.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ISA 17.32 1.17 18.50
ISA.sweep 14.53 0.83 15.36
ISA.iterate 9.72 0.41 10.13
ISA.unique 8.78 0.17 8.96
ISA.GO 6.41 0.27 6.67
eisa.biclust 5.08 0.20 5.40
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/eisa.Rcheck/00check.log'
for details.
eisa.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/eisa_1.40.0.tar.gz && rm -rf eisa.buildbin-libdir && mkdir eisa.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eisa.buildbin-libdir eisa_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL eisa_1.40.0.zip && rm eisa_1.40.0.tar.gz eisa_1.40.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1197k 100 1197k 0 0 15.3M 0 --:--:-- --:--:-- --:--:-- 16.9M
install for i386
* installing *source* package 'eisa' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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
converting help for package 'eisa'
finding HTML links ... done
ALLModules html
ISA.CHR html
ISA.GO html
ISA.KEGG html
ISA html
ISA.html html
ISA.iterate html
ISA.miRNA html
ISA.normalize html
ISA.sweep html
ISA.unique html
ISA2heatmap html
ISAExpressionSet html
ISAModules-class html
ListHyperGParams-class html
ListHyperGResult-class html
cond.plot html
eisa.biclust html
enrichment html
exp.plot html
gograph html
mnplot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/mnplot.Rd:36: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
overlap html
profilePlot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/profilePlot.Rd:45: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMTkhFz/R.INSTALL1a0c287336d6/eisa/man/profilePlot.Rd:47: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
robustness html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'eisa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eisa' as eisa_1.40.0.zip
* DONE (eisa)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'eisa' successfully unpacked and MD5 sums checked
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eisa.Rcheck/examples_i386/eisa-Ex.timings
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eisa.Rcheck/examples_x64/eisa-Ex.timings
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