siggenes 1.49.0
Holger Schwender
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/siggenes | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings siggenes_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/siggenes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.49.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘siggenes’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘splines’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘KernSmooth’ ‘affy’ ‘annotate’ ‘scrime’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.C("get_stat_num_denum", ..., PACKAGE = "multtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
cat.null.approx: no visible global function definition for ‘qchisq’
cat.null.approx: no visible global function definition for ‘pchisq’
cat.null.approx2: no visible global function definition for ‘pchisq’
cat.null.approx2: no visible global function definition for ‘dchisq’
checkA0: no visible global function definition for ‘quantile’
checkDBs: no visible global function definition for ‘getAnnMap’
checkQuantiles: no visible global function definition for ‘quantile’
chisqEbamMissing: no visible global function definition for
‘rowChisq2Class’
chisqEbamMissing: no visible global function definition for
‘rowChisqMultiClass’
chisqStatMissing: no visible global function definition for
‘rowChisq2Class’
chisqStatMissing: no visible global function definition for
‘rowChisqMultiClass’
chisqStatMissing: no visible global function definition for ‘qchisq’
col2hex: no visible global function definition for ‘col2rgb’
compFailABF: no visible global function definition for ‘dnorm’
compRatio: no visible global function definition for ‘glm’
compRatio: no visible binding for global variable ‘binomial’
compRatio: no visible global function definition for ‘predict’
d.null: no visible binding for global variable ‘median’
delta.plot: no visible global function definition for ‘par’
delta.plot: no visible global function definition for ‘segments’
denspr: no visible global function definition for ‘hist’
denspr: no visible global function definition for ‘quantile’
denspr: no visible global function definition for ‘glm’
denspr: no visible binding for global variable ‘poisson’
denspr: no visible global function definition for ‘predict’
find.a0: no visible global function definition for ‘qnorm’
finda02html: no visible global function definition for ‘par’
finda02html: no visible global function definition for ‘dev.off’
fudge2: no visible global function definition for ‘quantile’
fudge2: no visible binding for global variable ‘mad’
fudge2 : cv: no visible global function definition for ‘sd’
fuzzy.ebam: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.ebam: no visible global function definition for ‘dnorm’
fuzzy.ebam: no visible global function definition for ‘qnorm’
fuzzy.ebam: no visible global function definition for ‘abf’
fuzzy.null.abf: no visible global function definition for ‘dnorm’
fuzzy.null.approx: no visible global function definition for
‘na.exclude’
fuzzy.null.approx: no visible global function definition for ‘qnorm’
fuzzy.stat: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.stat: no visible global function definition for ‘qnorm’
fuzzy.stat: no visible global function definition for ‘abf’
getFailure: no visible global function definition for ‘approx’
help.ebam: no visible global function definition for ‘browseURL’
help.finda0: no visible global function definition for ‘browseURL’
help.sam: no visible global function definition for ‘browseURL’
limma2ebam: no visible global function definition for ‘pt’
limma2ebam: no visible global function definition for ‘dt’
limma2sam: no visible global function definition for ‘pt’
limma2sam: no visible global function definition for ‘qt’
limma2sam: no visible global function definition for ‘ppoints’
limma2sam: no visible global function definition for ‘na.exclude’
lines.denspr: no visible global function definition for ‘lines’
make.tablecode: no visible global function definition for
‘cleancdfname’
make.tablecode: no visible global function definition for ‘geneNames’
make.tablecode: no visible global function definition for ‘lookUp’
make.tablecode: no visible global function definition for
‘shortenGeneDescription’
md.plot: no visible global function definition for ‘par’
md.plot: no visible global function definition for ‘points’
nclass.wand: no visible global function definition for ‘dpih’
pi0.est: no visible global function definition for ‘smooth.spline’
pi0.est: no visible global function definition for ‘predict’
plotLegendLines: no visible global function definition for ‘abline’
plotLegendLines: no visible global function definition for ‘legend’
plotLegendLines: no visible global function definition for ‘segments’
qvalue.cal: no visible global function definition for ‘na.exclude’
sam: no visible global function definition for ‘na.exclude’
sam.plot2: no visible global function definition for ‘par’
sam.plot2: no visible global function definition for ‘points’
sam.plot2: no visible global function definition for ‘abline’
sam.plot2: no visible global function definition for ‘text’
siggenes2html: no visible global function definition for ‘par’
siggenes2html: no visible global function definition for ‘dev.off’
stats.cal: no visible global function definition for ‘na.exclude’
trend.ebam.default: no visible global function definition for ‘sd’
trend.ebam.list: no visible global function definition for ‘rowCATTs’
trend.ebam.list: no visible global function definition for
‘rowMsquares’
trend.stat.default: no visible global function definition for ‘sd’
trend.stat.list: no visible global function definition for ‘rowCATTs’
trend.stat.list: no visible global function definition for
‘rowMsquares’
trend.stat.list: no visible global function definition for ‘qchisq’
wilc.ebam: no visible global function definition for ‘dwilcox’
wilc.ebam: no visible global function definition for ‘pwilcox’
wilc.ebam: no visible global function definition for ‘dnorm’
wilc.ebam: no visible global function definition for ‘pnorm’
wilc.ebam: no visible global function definition for ‘dsignrank’
wilc.ebam: no visible global function definition for ‘psignrank’
wilc.ebam: no visible global function definition for ‘glm’
wilc.ebam: no visible binding for global variable ‘poisson’
wilc.stat: no visible global function definition for ‘qwilcox’
wilc.stat: no visible global function definition for ‘pwilcox’
wilc.stat: no visible global function definition for ‘qnorm’
wilc.stat: no visible global function definition for ‘pnorm’
wilc.stat: no visible global function definition for ‘qsignrank’
wilc.stat: no visible global function definition for ‘psignrank’
z.find: no visible global function definition for ‘qf’
z.find: no visible global function definition for ‘qnorm’
identify,SAM: no visible global function definition for ‘text’
identify,SAM: no visible global function definition for ‘na.exclude’
identify,SAM: no visible global function definition for ‘lookUp’
identify,SAM: no visible global function definition for ‘getSYMBOL’
identify,SAM: no visible global function definition for ‘browseURL’
plot,EBAM-ANY: no visible global function definition for ‘points’
plot,EBAM-ANY: no visible global function definition for ‘abline’
plot,EBAM-ANY: no visible global function definition for ‘legend’
plot,FindA0-ANY: no visible global function definition for ‘lines’
plot,FindA0-ANY: no visible global function definition for ‘abline’
plot,FindA0-ANY: no visible global function definition for ‘legend’
print,sumEBAM: no visible global function definition for ‘write.table’
print,sumSAM: no visible global function definition for ‘write.table’
summary,EBAM: no visible global function definition for ‘lookUp’
summary,EBAM: no visible global function definition for ‘getSYMBOL’
summary,SAM: no visible global function definition for ‘p.adjust’
summary,SAM: no visible global function definition for ‘lookUp’
summary,SAM: no visible global function definition for ‘getSYMBOL’
Undefined global functions or variables:
abf abline approx binomial browseURL cleancdfname col2rgb dchisq
dev.off dnorm dpih dsignrank dt dwilcox geneNames getAnnMap getSYMBOL
glm hist legend lines lookUp mad median na.exclude p.adjust par
pchisq pnorm points poisson ppoints predict psignrank pt pwilcox
qchisq qf qnorm qsignrank qt quantile qwilcox rowCATTs rowChisq2Class
rowChisqMultiClass rowMsquares rowTrendFuzzy sd segments
shortenGeneDescription smooth.spline text write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.off")
importFrom("graphics", "abline", "hist", "legend", "lines", "par",
"points", "segments", "text")
importFrom("stats", "approx", "binomial", "dchisq", "dnorm",
"dsignrank", "dt", "dwilcox", "glm", "mad", "median",
"na.exclude", "p.adjust", "pchisq", "pnorm", "poisson",
"ppoints", "predict", "psignrank", "pt", "pwilcox",
"qchisq", "qf", "qnorm", "qsignrank", "qt", "quantile",
"qwilcox", "sd", "smooth.spline")
importFrom("utils", "browseURL", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/siggenes.Rcheck/00check.log’
for details.