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CHECK report for dyebias on tokay2

This page was generated on 2019-10-16 12:22:30 -0400 (Wed, 16 Oct 2019).

Package 473/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebias 1.44.0
Philip Lijnzaad
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/dyebias
Branch: RELEASE_3_9
Last Commit: 873346e
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dyebias
Version: 1.44.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dyebias.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dyebias_1.44.0.tar.gz
StartedAt: 2019-10-16 03:25:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:26:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 70.2 seconds
RetCode: 0
Status:  OK  
CheckDir: dyebias.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dyebias.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dyebias_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dyebias.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dyebias/DESCRIPTION' ... OK
* this is package 'dyebias' version '1.44.0'
* 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 'dyebias' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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' calls in package code:
  'limma' 'methods'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'marray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.check.reporter.labels: no visible global function definition for
  'maLabels'
.check.reporter.labels: no visible global function definition for
  'maGnames'
.check.reporter.labels: no visible global function definition for
  'maNspots'
.check.slide.labels: no visible global function definition for
  'maNsamples'
.check.slide.labels: no visible global function definition for
  'maLabels'
.check.slide.labels: no visible global function definition for
  'maTargets'
.find.estimators: no visible global function definition for 'quantile'
.limma.to.dataframe: no visible global function definition for 'is'
.limma.to.dataframe: no visible global function definition for 'eBayes'
.limma.to.dataframe: no visible global function definition for
  'p.adjust'
.mann.kendall: no visible global function definition for 'cor.test'
.merge.dyebias: no visible global function definition for 'maLabels'
.merge.dyebias: no visible global function definition for 'maGnames'
.monotonicity: no visible global function definition for 'maNsamples'
.monotonicity : : no visible global function definition for
  'maM'
.monotonicity : slope: no visible global function definition for
  'lsfit'
.rg.subsets: no visible global function definition for 'quantile'
.set.design: no visible global function definition for 'modelMatrix'
.set.design : : no visible global function definition for
  'modelMatrix'
.set.output: no visible global function definition for 'X11'
.set.output: no visible global function definition for 'windows'
.set.output: no visible global function definition for 'pdf'
.set.output: no visible global function definition for 'png'
.set.output: no visible global function definition for 'postscript'
.slide.bias: no visible global function definition for 'maNsamples'
.slide.bias: no visible global function definition for 'maLabels'
.slide.bias: no visible global function definition for 'maTargets'
.slide.bias: no visible global function definition for 'maM'
.slide.bias.order: no visible binding for global variable 'median'
dyebias.application.subset: no visible global function definition for
  'maInfo'
dyebias.application.subset: no visible global function definition for
  'maTargets'
dyebias.application.subset: no visible global function definition for
  'maNspots'
dyebias.application.subset: no visible global function definition for
  'maNsamples'
dyebias.application.subset: no visible global function definition for
  'maRb'
dyebias.application.subset: no visible global function definition for
  'maGb'
dyebias.application.subset: no visible global function definition for
  'maRf'
dyebias.application.subset: no visible global function definition for
  'maGf'
dyebias.apply.correction: no visible global function definition for
  'maM'
dyebias.apply.correction: no visible global function definition for
  'maNspots'
dyebias.apply.correction: no visible global function definition for
  'maNsamples'
dyebias.apply.correction: no visible global function definition for
  'maLabels'
dyebias.apply.correction: no visible global function definition for
  'maGnames'
dyebias.apply.correction: no visible global function definition for
  'maInfo'
dyebias.apply.correction: no visible global function definition for
  'maTargets'
dyebias.apply.correction: no visible global function definition for
  'median'
dyebias.apply.correction: no visible global function definition for
  'sd'
dyebias.apply.correction: no visible global function definition for
  'var.test'
dyebias.apply.correction: no visible global function definition for
  'maA'
dyebias.apply.correction: no visible global function definition for
  'maM<-'
dyebias.apply.correction: no visible global function definition for
  'maA<-'
dyebias.apply.correction: no visible global function definition for
  'is'
dyebias.apply.correction: no visible global function definition for
  'maR<-'
dyebias.apply.correction: no visible global function definition for
  'maG<-'
dyebias.boxplot: no visible global function definition for 'maNsamples'
dyebias.boxplot: no visible global function definition for 'par'
dyebias.boxplot: no visible global function definition for 'boxplot'
dyebias.boxplot: no visible global function definition for 'abline'
dyebias.boxplot: no visible global function definition for 'dev.off'
dyebias.estimate.iGSDBs: no visible global function definition for 'is'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maLabels'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maGnames'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maNspots'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maNsamples'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maM'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maA'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maInfo'
dyebias.estimate.iGSDBs: no visible global function definition for
  'maTargets'
dyebias.estimate.iGSDBs: no visible global function definition for
  'new'
dyebias.estimate.iGSDBs: no visible global function definition for
  'lmFit'
dyebias.estimate.iGSDBs: no visible global function definition for
  'eBayes'
dyebias.maplot: no visible global function definition for 'maM'
dyebias.maplot: no visible global function definition for 'maA'
dyebias.maplot: no visible global function definition for 'plot'
dyebias.maplot: no visible global function definition for 'box'
dyebias.maplot: no visible global function definition for 'abline'
dyebias.maplot: no visible global function definition for 'points'
dyebias.maplot: no visible global function definition for 'dev.off'
dyebias.monotonicityplot: no visible global function definition for
  'plot'
dyebias.monotonicityplot: no visible global function definition for
  'points'
dyebias.monotonicityplot: no visible global function definition for
  'dev.off'
dyebias.rgplot: no visible global function definition for 'maA'
dyebias.rgplot: no visible global function definition for 'maM'
dyebias.rgplot: no visible global function definition for 'plot'
dyebias.rgplot: no visible global function definition for 'axis'
dyebias.rgplot: no visible global function definition for 'box'
dyebias.rgplot: no visible global function definition for 'abline'
dyebias.rgplot: no visible global function definition for 'points'
dyebias.rgplot: no visible global function definition for 'dev.off'
dyebias.trendplot: no visible global function definition for 'quantile'
dyebias.trendplot: no visible global function definition for
  'maNsamples'
dyebias.trendplot : : no visible global function definition
  for 'maM'
dyebias.trendplot: no visible binding for global variable 'median'
dyebias.trendplot: no visible global function definition for 'matplot'
dyebias.trendplot: no visible global function definition for 'axis'
dyebias.trendplot: no visible global function definition for 'matlines'
dyebias.trendplot: no visible global function definition for 'abline'
dyebias.trendplot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  X11 abline axis box boxplot cor.test dev.off eBayes is lmFit lsfit
  maA maA<- maG<- maGb maGf maGnames maInfo maLabels maM maM<-
  maNsamples maNspots maR<- maRb maRf maTargets matlines matplot median
  modelMatrix new p.adjust par pdf plot png points postscript quantile
  sd var.test windows
Consider adding
  importFrom("grDevices", "X11", "dev.off", "pdf", "png", "postscript",
             "windows")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "matlines",
             "matplot", "par", "plot", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "cor.test", "lsfit", "median", "p.adjust",
             "quantile", "sd", "var.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/dyebias.Rcheck/00check.log'
for details.



Installation output

dyebias.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/dyebias_1.44.0.tar.gz && rm -rf dyebias.buildbin-libdir && mkdir dyebias.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dyebias.buildbin-libdir dyebias_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL dyebias_1.44.0.zip && rm dyebias_1.44.0.tar.gz dyebias_1.44.0.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  578k  100  578k    0     0  4334k      0 --:--:-- --:--:-- --:--:-- 4553k

install for i386

* installing *source* package 'dyebias' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dyebias'
    finding HTML links ... done
    dyebias-package                         html  
    dyebias.application.subset              html  
    dyebias.apply.correction                html  
    dyebias.boxplot                         html  
    dyebias.estimate.iGSDBs                 html  
    dyebias.monotonicity                    html  
    dyebias.monotonicityplot                html  
    dyebias.rgplot                          html  
    dyebias.trendplot                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'dyebias' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dyebias' as dyebias_1.44.0.zip
* DONE (dyebias)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'dyebias' successfully unpacked and MD5 sums checked

Tests output


Example timings

dyebias.Rcheck/examples_i386/dyebias-Ex.timings

nameusersystemelapsed
dyebias.application.subset2.110.162.98
dyebias.apply.correction2.310.002.32
dyebias.boxplot1.940.062.01
dyebias.estimate.iGSDBs1.360.001.36
dyebias.monotonicity000
dyebias.monotonicityplot000
dyebias.rgplot2.300.012.31
dyebias.trendplot1.890.021.91

dyebias.Rcheck/examples_x64/dyebias-Ex.timings

nameusersystemelapsed
dyebias.application.subset2.280.142.42
dyebias.apply.correction1.550.001.55
dyebias.boxplot1.840.011.86
dyebias.estimate.iGSDBs1.20.01.2
dyebias.monotonicity000
dyebias.monotonicityplot000
dyebias.rgplot2.50.12.6
dyebias.trendplot2.140.002.14