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BioC 3.4: CHECK report for siggenes on morelia

This page was generated on 2017-04-15 16:21:48 -0400 (Sat, 15 Apr 2017).

Package 1142/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
siggenes 1.48.0
Holger Schwender
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/siggenes
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: siggenes
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings siggenes_1.48.0.tar.gz
StartedAt: 2017-04-15 08:08:55 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:10:19 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 83.2 seconds
RetCode: 0
Status:  OK 
CheckDir: siggenes.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings siggenes_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/siggenes.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.48.0’
* 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-3.4-bioc/meat/siggenes.Rcheck/00check.log’
for details.


siggenes.Rcheck/00install.out:

* installing *source* package ‘siggenes’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (siggenes)

siggenes.Rcheck/siggenes-Ex.timings:

nameusersystemelapsed
EBAM-class000
SAM-class0.0020.0010.001
chisq.ebam0.0010.0000.001
chisq.stat0.0010.0000.001
delta.plot0.0010.0000.001
denspr0.0000.0000.001
ebam0.0030.0000.003
find.a00.0010.0010.002
help.ebam0.0010.0000.001
help.finda00.0010.0000.000
help.sam0.0000.0000.001
list.siggenes0.0010.0000.001
md.plot0.0010.0000.001
pi0.est0.0000.0000.001
qvalue.cal0.0010.0010.001
sam0.0030.0000.003
sam.plot20.0010.0000.001
trend.ebam0.0020.0000.001
trend.stat0.0010.0000.002