ToPASeq 1.7.0
Ivana Ihnatova
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ToPASeq | | Last Changed Rev: 120823 / Revision: 121152 | | Last Changed Date: 2016-09-09 09:20:44 -0700 (Fri, 09 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ToPASeq_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ToPASeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToPASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToPASeq’ version ‘1.7.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ToPASeq’ 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
* 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:
‘DEGraph’ ‘plotrix’
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
.hote: no visible global function definition for ‘cov’
.hote: no visible global function definition for ‘pf’
.hotePaired: no visible global function definition for ‘cov’
.runCliqueVarTest: no visible global function definition for ‘pchisq’
.runPathwayVarTest: no visible global function definition for ‘qchisq’
.runPathwayVarTest: no visible global function definition for ‘pchisq’
CLIPPER: no visible global function definition for ‘p.adjust’
CLIPPERfast: no visible global function definition for ‘p.adjust’
CMT: no visible global function definition for ‘pf’
CMT: no visible global function definition for ‘t.test’
KEGG2Pathway : <anonymous>: no visible global function definition for
‘combn’
KEGG2Pathway: no visible binding for global variable ‘title’
PRSSingle : <anonymous>: no visible global function definition for
‘setNames’
PRSSingle: no visible global function definition for ‘sd’
PRSweights: no visible global function definition for ‘setNames’
SPIA4plot: no visible global function definition for ‘median’
SPIASingle: no visible global function definition for ‘median’
SPIASingle: no visible global function definition for ‘phyper’
SPIAweights: no visible global function definition for ‘setNames’
TAPPA: no visible binding for global variable ‘t.test’
TIF: no visible global function definition for ‘cor’
adjustAttr: no visible global function definition for ‘setNames’
adjustAttrCli : <anonymous>: no visible global function definition for
‘combn’
adjustAttrCli : <anonymous>: no visible global function definition for
‘setNames’
adjustAttrCli: no visible global function definition for ‘setNames’
applyTh: no visible global function definition for ‘setNames’
checkPkgVersion: no visible global function definition for
‘installed.packages’
combfunc: no visible global function definition for ‘na.omit’
combfunc: no visible global function definition for ‘pnorm’
combfunc: no visible global function definition for ‘qnorm’
convertIdentifiersByVector: no visible global function definition for
‘setNames’
degraph: no visible global function definition for ‘p.adjust’
drawGraph: no visible global function definition for ‘layout’
drawHead : normArrow: no visible global function definition for
‘polygon’
drawHead: no visible global function definition for ‘polygon’
drawHead: no visible global function definition for ‘symbols’
drawHead: no visible global function definition for ‘arrows’
drawNodesPies2: no visible global function definition for ‘strwidth’
drawNodesPies2: no visible global function definition for ‘strheight’
drawNodesPies2: no visible global function definition for ‘text’
drawSPIA: no visible global function definition for ‘par’
drawSPIA: no visible global function definition for ‘abline’
drawSPIA: no visible global function definition for ‘points’
drawSPIA: no visible global function definition for ‘legend’
drawSPIA: no visible global function definition for ‘text’
drawSPIA: no visible global function definition for ‘density’
drawSPIA: no visible global function definition for ‘sd’
edgetypeslegend: no visible global function definition for ‘par’
edgetypeslegend: no visible global function definition for ‘text’
edgetypeslegend: no visible global function definition for ‘legend’
getNodeCex: no visible global function definition for ‘strwidth’
getNodeCex: no visible global function definition for ‘strheight’
headline: no visible global function definition for ‘title’
isComplex: no visible global function definition for ‘combn’
makeEdgeList: no visible global function definition for ‘setNames’
makeNodeSizeLegend: no visible global function definition for
‘setNames’
normalizationTAPPA : <anonymous>: no visible global function definition
for ‘sd’
notPTIF: no visible global function definition for ‘rbinom’
notPTIF: no visible global function definition for ‘rnorm’
notPTIF: no visible global function definition for ‘sd’
pieRad: no visible global function definition for ‘par’
pieRad: no visible global function definition for ‘polygon’
plot.topResult: no visible global function definition for
‘colorRampPalette’
plot.topResult: no visible global function definition for ‘setNames’
plotCliques: no visible global function definition for ‘setNames’
plotCliques: no visible global function definition for ‘par’
plotCliques: no visible global function definition for ‘legend’
plotRagraph : .local: no visible global function definition for
‘plot.new’
plotRagraph : .local: no visible global function definition for ‘par’
plotRagraph : .local: no visible global function definition for
‘strheight’
plotRagraph : .local: no visible global function definition for ‘title’
plotRagraph : .local: no visible global function definition for
‘plot.window’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘strwidth’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘strheight’
processRNAseq: no visible global function definition for ‘model.matrix’
prs: no visible global function definition for ‘p.adjust’
pwea: no visible global function definition for ‘p.adjust’
renderEdgesTypes2: no visible global function definition for ‘par’
renderOrig: no visible global function definition for ‘setNames’
renderReduced: no visible global function definition for ‘setNames’
spia: no visible global function definition for ‘p.adjust’
tappa: no visible global function definition for ‘p.adjust’
testMA: no visible global function definition for ‘model.matrix’
testvoomlimma: no visible global function definition for ‘model.matrix’
testvstlimma: no visible global function definition for ‘model.matrix’
topologyGSA: no visible global function definition for ‘p.adjust’
degree,Pathway-character: no visible global function definition for
‘setNames’
nodes<-,Pathway-character: no visible global function definition for
‘setNames’
Undefined global functions or variables:
abline arrows colorRampPalette combn cor cov density
installed.packages layout legend median model.matrix na.omit p.adjust
par pchisq pf phyper plot.new plot.window pnorm points polygon qchisq
qnorm rbinom rnorm sd setNames strheight strwidth symbols t.test text
title
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "abline", "arrows", "layout", "legend", "par",
"plot.new", "plot.window", "points", "polygon", "strheight",
"strwidth", "symbols", "text", "title")
importFrom("stats", "cor", "cov", "density", "median", "model.matrix",
"na.omit", "p.adjust", "pchisq", "pf", "phyper", "pnorm",
"qchisq", "qnorm", "rbinom", "rnorm", "sd", "setNames",
"t.test")
importFrom("utils", "combn", "installed.packages")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘ToPASeq.pdf’ from 879Kb to 780Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Clipper 16.728 0.056 16.838
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/ToPASeq.Rcheck/00check.log’
for details.
* installing *source* package ‘ToPASeq’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c accCpp.cpp -o accCpp.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c colMinMax.cpp -o colMinMax.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c downstream.cpp -o downstream.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o ToPASeq.so RcppExports.o accCpp.o colMinMax.o downstream.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/ToPASeq.Rcheck/ToPASeq/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘numNoEdges’ from package ‘graph’ in package ‘ToPASeq’
Creating a generic function for ‘mostEdges’ from package ‘graph’ in package ‘ToPASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ToPASeq)