Package: siggenes

Version: 1.52.0

Command: rm -rf siggenes.buildbin-libdir siggenes.Rcheck && mkdir siggenes.buildbin-libdir siggenes.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=siggenes.buildbin-libdir siggenes_1.52.0.tar.gz >siggenes.Rcheck\00install.out 2>&1 && cp siggenes.Rcheck\00install.out siggenes-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=siggenes.buildbin-libdir --install="check:siggenes-install.out" --force-multiarch --no-vignettes --timings siggenes_1.52.0.tar.gz

StartedAt: 2018-04-12 03:11:04 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:12:43 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 98.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: siggenes.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf siggenes.buildbin-libdir siggenes.Rcheck && mkdir siggenes.buildbin-libdir siggenes.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=siggenes.buildbin-libdir siggenes_1.52.0.tar.gz >siggenes.Rcheck\00install.out 2>&1 && cp siggenes.Rcheck\00install.out siggenes-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=siggenes.buildbin-libdir --install="check:siggenes-install.out" --force-multiarch --no-vignettes --timings siggenes_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/siggenes.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.52.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuQAUdh/R.INSTALL2ac8d9c3309/siggenes/man/fuzzy.ebam.Rd:29: missing file link 'getMatFuzzy'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/siggenes.Rcheck/00install.out' for details.
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/siggenes.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'siggenes' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'siggenes'
    finding HTML links ... done
    EBAM-class                              html  
    FindA0-class                            html  
    SAM-class                               html  
    chisq.ebam                              html  
    chisq.stat                              html  
    d.stat                                  html  
    delta.plot                              html  
    denspr                                  html  
    ebam                                    html  
    ebamControl                             html  
    find.a0                                 html  
    findDelta                               html  
    fudge2                                  html  
    fuzzy.ebam                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpuQAUdh/R.INSTALL2ac8d9c3309/siggenes/man/fuzzy.ebam.Rd:29: missing file link 'getMatFuzzy'
    help.ebam                               html  
    help.finda0                             html  
    help.sam                                html  
    limma2sam                               html  
    link.genes                              html  
    link.siggenes                           html  
    list.siggenes                           html  
    md.plot                                 html  
    nclass.wand                             html  
    pi0.est                                 html  
    plotArguments                           html  
    plotFindArguments                       html  
    qvalue.cal                              html  
    rowWilcoxon                             html  
    sam                                     html  
    sam.plot2                               html  
    samControl                              html  
    siggenes-internal                       html  
    siggenes2excel                          html  
    siggenes2html                           html  
    sumSAM-class                            html  
    trend.ebam                              html  
    trend.stat                              html  
    wilc.ebam                               html  
    wilc.stat                               html  
    z.ebam                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'siggenes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'siggenes' as siggenes_1.52.0.zip
* DONE (siggenes)
In R CMD INSTALL
In R CMD INSTALL