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CHECK report for siggenes on tokay2

This page was generated on 2018-10-17 08:31:55 -0400 (Wed, 17 Oct 2018).

Package 1367/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
siggenes 1.54.0
Holger Schwender
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/siggenes
Branch: RELEASE_3_7
Last Commit: 1630e42
Last Changed Date: 2018-04-30 10:34:57 -0400 (Mon, 30 Apr 2018)
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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: siggenes
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:siggenes.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings siggenes_1.54.0.tar.gz
StartedAt: 2018-10-17 04:51:00 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:52:42 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 101.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: siggenes.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:siggenes.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings siggenes_1.54.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/siggenes.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.54.0'
* 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-3.7-bioc/tmpdir/Rtmpwn4plG/R.INSTALL11146e4b45c5/siggenes/man/fuzzy.ebam.Rd:29: file link 'getMatFuzzy' in package 'scrime' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 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-3.7-bioc/meat/siggenes.Rcheck/00check.log'
for details.



Installation output

siggenes.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/siggenes_1.54.0.tar.gz && rm -rf siggenes.buildbin-libdir && mkdir siggenes.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=siggenes.buildbin-libdir siggenes_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL siggenes_1.54.0.zip && rm siggenes_1.54.0.tar.gz siggenes_1.54.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  589k  100  589k    0     0  8330k      0 --:--:-- --:--:-- --:--:-- 9361k

install for i386

* installing *source* package 'siggenes' ...
** R
** byte-compile and prepare 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-3.7-bioc/tmpdir/Rtmpwn4plG/R.INSTALL11146e4b45c5/siggenes/man/fuzzy.ebam.Rd:29: file link 'getMatFuzzy' in package 'scrime' does not exist and so has been treated as a topic
    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_1.54.0.zip
* DONE (siggenes)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'siggenes' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

siggenes.Rcheck/examples_i386/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.plot000
pi0.est000
qvalue.cal000
sam000
sam.plot2000
trend.ebam000
trend.stat0.000.020.01

siggenes.Rcheck/examples_x64/siggenes-Ex.timings

nameusersystemelapsed
EBAM-class000
SAM-class0.010.000.01
chisq.ebam000
chisq.stat0.020.000.02
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