CoRegNet 1.13.0
Remy Nicolle
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CoRegNet | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf CoRegNet.buildbin-libdir CoRegNet.Rcheck && mkdir CoRegNet.buildbin-libdir CoRegNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoRegNet.buildbin-libdir CoRegNet_1.13.0.tar.gz >CoRegNet.Rcheck\00install.out 2>&1 && cp CoRegNet.Rcheck\00install.out CoRegNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CoRegNet.buildbin-libdir --install="check:CoRegNet-install.out" --force-multiarch --no-vignettes --timings CoRegNet_1.13.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoRegNet.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoRegNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoRegNet' version '1.13.0'
* 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 'CoRegNet' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'RColorBrewer' 'gplots'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.descriptionUpdate: no visible global function definition for 'vcount'
.descriptionUpdate: no visible global function definition for
'fisher.test'
.distfun: no visible global function definition for 'as.dist'
.distfun: no visible global function definition for 'cor'
.fitGRN : <anonymous>: no visible global function definition for 'lm'
.fitGRN : <anonymous>: no visible global function definition for 'coef'
.fitGRN: no visible global function definition for 'cor'
.fitGRN: no visible global function definition for 'lm'
.fitGRN: no visible global function definition for 'coef'
.hclustfun: no visible global function definition for 'hclust'
.heatplot: no visible global function definition for 'rainbow'
.heatplot : distf: no visible global function definition for 'as.dist'
.heatplot : distf: no visible global function definition for 'cor'
.heatplot : hclustf: no visible global function definition for 'hclust'
.heatplot: no visible global function definition for 'colorRampPalette'
.heatplot: no visible global function definition for 'heatmap.2'
.heatplot: no visible global function definition for 'quantile'
.tfPlot: no visible global function definition for 'colorRampPalette'
.tfPlot: no visible global function definition for 'rainbow'
.tfPlot: no visible global function definition for 'par'
.tfPlot: no visible global function definition for 'mtext'
.tfPlot: no visible global function definition for 'quantile'
.traits : <anonymous>: no visible global function definition for
'lines'
.traits: no visible global function definition for 'abline'
automaticParameters: no visible global function definition for
'quantile'
automaticParameters : <anonymous>: no visible global function
definition for 'pnorm'
automaticParameters: no visible global function definition for 'plot'
automaticParameters: no visible global function definition for 'abline'
automaticParameters: no visible global function definition for 'sd'
coregnet : <anonymous>: no visible global function definition for 'cor'
coregnet: no visible global function definition for 'cor'
directedNetworkEnrichment: no visible global function definition for
'fisher.test'
discretizeExpressionData: no visible global function definition for
'sd'
fishersMethod: no visible global function definition for 'pchisq'
legendPlot: no visible global function definition for 'par'
legendPlot: no visible global function definition for
'colorRampPalette'
legendPlot: no visible global function definition for 'axis'
legendPlot: no visible global function definition for 'rainbow'
list.enriched: no visible global function definition for 'wilcox.test'
networkLegendPlot: no visible global function definition for 'par'
networkLegendPlot: no visible global function definition for 'plot'
networkLegendPlot: no visible global function definition for 'symbols'
networkLegendPlot: no visible global function definition for 'text'
networkLegendPlot: no visible global function definition for 'rainbow'
networkLegendPlot: no visible global function definition for 'segments'
networkLegendPlot: no visible global function definition for 'arrows'
reactiveAdjacencyMatrix : <anonymous>: no visible global function
definition for 'rainbow'
set.overlap: no visible global function definition for 'fisher.test'
undirectedNetworkEnrichment: no visible global function definition for
'fisher.test'
updateData : <anonymous> : <anonymous>: no visible global function
definition for 't.test'
activators,coregnet: no visible global function definition for
'na.omit'
coregulators,coregnet: no visible global function definition for
'p.adjust'
coregulators,coregnet : <anonymous>: no visible global function
definition for 'fisher.test'
refine,coregnet: no visible global function definition for 'glm'
refine,coregnet: no visible global function definition for 'plot'
refine,coregnet: no visible global function definition for 'abline'
regulatorInfluence,coregnet : <anonymous> : <anonymous>: no visible
global function definition for 't.test'
regulators,coregnet: no visible global function definition for
'na.omit'
repressors,coregnet: no visible global function definition for
'na.omit'
targets,coregnet: no visible global function definition for 'na.omit'
Undefined global functions or variables:
abline arrows as.dist axis coef colorRampPalette cor fisher.test glm
hclust heatmap.2 lines lm mtext na.omit p.adjust par pchisq plot
pnorm quantile rainbow sd segments symbols t.test text vcount
wilcox.test
Consider adding
importFrom("grDevices", "colorRampPalette", "rainbow")
importFrom("graphics", "abline", "arrows", "axis", "lines", "mtext",
"par", "plot", "segments", "symbols", "text")
importFrom("stats", "as.dist", "coef", "cor", "fisher.test", "glm",
"hclust", "lm", "na.omit", "p.adjust", "pchisq", "pnorm",
"quantile", "sd", "t.test", "wilcox.test")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoRegNet.buildbin-libdir/CoRegNet/libs/i386/CoRegNet.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
hLICORN 20.92 0 20.92
masterRegulator 8.19 0 8.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
hLICORN 30.28 0 30.28
masterRegulator 11.13 0 11.13
* checking for unstated dependencies in 'tests' ... WARNING
'::' or ':::' import not declared from: 'BiocGenerics'
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/CoRegNet.Rcheck/00check.log'
for details.