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BioC 3.5: CHECK report for siggenes on tokay2

This page was generated on 2017-08-16 13:18:34 -0400 (Wed, 16 Aug 2017).

Package 1217/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
siggenes 1.50.0
Holger Schwender
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/siggenes
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: siggenes
Version: 1.50.0
Command: rm -rf siggenes.buildbin-libdir siggenes.Rcheck && mkdir siggenes.buildbin-libdir siggenes.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=siggenes.buildbin-libdir siggenes_1.50.0.tar.gz >siggenes.Rcheck\00install.out 2>&1 && cp siggenes.Rcheck\00install.out siggenes-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=siggenes.buildbin-libdir --install="check:siggenes-install.out" --force-multiarch --no-vignettes --timings siggenes_1.50.0.tar.gz
StartedAt: 2017-08-16 02:54:36 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:56:41 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 125.7 seconds
RetCode: 0
Status:  OK  
CheckDir: siggenes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf siggenes.buildbin-libdir siggenes.Rcheck && mkdir siggenes.buildbin-libdir siggenes.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=siggenes.buildbin-libdir siggenes_1.50.0.tar.gz >siggenes.Rcheck\00install.out 2>&1 && cp siggenes.Rcheck\00install.out siggenes-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=siggenes.buildbin-libdir --install="check:siggenes-install.out" --force-multiarch --no-vignettes --timings siggenes_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/siggenes.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 'siggenes/DESCRIPTION' ... OK
* this is package 'siggenes' version '1.50.0'
* 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 '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
* 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' 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
.onAttach: no visible global function definition for 'winMenuAddItem'
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 winMenuAddItem 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", "winMenuAddItem", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/siggenes.Rcheck/00check.log'
for details.


siggenes.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'siggenes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'siggenes' as siggenes_1.50.0.zip
* DONE (siggenes)

siggenes.Rcheck/examples_i386/siggenes-Ex.timings:

nameusersystemelapsed
EBAM-class000
SAM-class0.010.000.02
chisq.ebam000
chisq.stat000
delta.plot000
denspr000
ebam000
find.a0000
help.ebam000
help.finda0000
help.sam000
list.siggenes000
md.plot000
pi0.est000
qvalue.cal000
sam000
sam.plot2000
trend.ebam000
trend.stat000

siggenes.Rcheck/examples_x64/siggenes-Ex.timings:

nameusersystemelapsed
EBAM-class000
SAM-class000
chisq.ebam000
chisq.stat000
delta.plot000
denspr000
ebam000
find.a0000
help.ebam000
help.finda0000
help.sam000
list.siggenes000
md.plot0.020.000.01
pi0.est000
qvalue.cal000
sam000
sam.plot20.010.000.02
trend.ebam000
trend.stat000