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CHECK report for charm on tokay1

This page was generated on 2019-04-13 11:21:10 -0400 (Sat, 13 Apr 2019).

Package 235/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
charm 2.28.0
Peter Murakami
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/charm
Branch: RELEASE_3_8
Last Commit: f6e6e9b
Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: charm
Version: 2.28.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:charm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings charm_2.28.0.tar.gz
StartedAt: 2019-04-13 01:07:39 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:28:14 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1234.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: charm.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:charm.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings charm_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/charm.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'charm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'charm' version '2.28.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'charm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'SQN' 'fields' 'genefilter'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'oligo:::pm'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Rug: no visible global function definition for 'Axis'
SQNff: no visible global function definition for 'Mclust'
arrayImage: no visible global function definition for
  'discretize.image'
arrayPlot: no visible global function definition for 'image.plot'
bgAdjustParameters: no visible global function definition for 'approx'
cmdsplot: no visible global function definition for 'pData'
cmdsplot: no visible global function definition for 'ffapply'
cmdsplot: no visible global function definition for 'rowSds'
cmdsplot: no visible global function definition for 'dist'
cmdsplot: no visible global function definition for 'cmdscale'
controlQC: no visible global function definition for 'pData'
controlQC: no visible global function definition for 'axis'
controlQC: no visible global function definition for 'segments'
controlQC: no visible global function definition for 'boxplot'
dmrFind: no visible global function definition for 'ffapply'
dmrFind: no visible global function definition for 'pt'
dmrPlot_paired: no visible global function definition for 'matplot'
dmrPlot_paired: no visible global function definition for 'matpoints'
dmrPlot_paired: no visible global function definition for 'matlines'
dmrPlot_paired: no visible global function definition for 'mtext'
dmrPlot_unpaired: no visible global function definition for 'matplot'
dmrPlot_unpaired: no visible global function definition for 'matlines'
dmrPlot_unpaired: no visible global function definition for 'mtext'
dosmooth: no visible global function definition for 'runmed'
edge.qvalue: no visible global function definition for 'smooth.spline'
get.tt.paired: no visible global function definition for 'rowVars'
plotDMRs: no visible global function definition for 'matplot'
plotDMRs: no visible global function definition for 'runmed'
plotRegions: no visible global function definition for 'matplot'
plotRegions: no visible global function definition for 'runmed'
plot_CpG: no visible global function definition for 'start'
plot_CpG: no visible global function definition for 'matchPattern'
regionMatch: no visible global function definition for 'IRanges'
regionPlot_paired: no visible global function definition for 'matplot'
regionPlot_paired: no visible global function definition for
  'matpoints'
regionPlot_paired: no visible global function definition for 'matlines'
regionPlot_paired: no visible global function definition for 'mtext'
regionPlot_unpaired: no visible global function definition for
  'matplot'
regionPlot_unpaired: no visible global function definition for
  'matlines'
regionPlot_unpaired: no visible global function definition for 'mtext'
rowCor: no visible global function definition for 'rowSds'
spatialAdjust: no visible global function definition for
  'discretize.image'
spatialAdjustVec: no visible global function definition for
  'image.smooth'
Undefined global functions or variables:
  Axis IRanges Mclust approx axis boxplot cmdscale discretize.image
  dist ffapply image.plot image.smooth matchPattern matlines matplot
  matpoints mtext pData pt rowSds rowVars runmed segments smooth.spline
  start
Consider adding
  importFrom("graphics", "Axis", "axis", "boxplot", "matlines",
             "matplot", "matpoints", "mtext", "segments")
  importFrom("stats", "approx", "cmdscale", "dist", "pt", "runmed",
             "smooth.spline", "start")
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' ... WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
Examples with CPU or elapsed time > 5s
              user system elapsed
qval        343.65   5.47  349.14
plotDensity   6.41   0.07    6.49
cpgdensity    5.08   0.33    5.41
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/charmData/data', resetting
Examples with CPU or elapsed time > 5s
              user system elapsed
qval        341.47   4.89  346.40
plotDensity   5.00   0.08    5.08
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/charm.Rcheck/00check.log'
for details.

Installation output

charm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/charm_2.28.0.tar.gz && rm -rf charm.buildbin-libdir && mkdir charm.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=charm.buildbin-libdir charm_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL charm_2.28.0.zip && rm charm_2.28.0.tar.gz charm_2.28.0.zip
###
##############################################################################
##############################################################################


  % 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 85704  100 85704    0     0   199k      0 --:--:-- --:--:-- --:--:--  201k

install for i386

* installing *source* package 'charm' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'charm'
    finding HTML links ... done
    bgAdjust                                html  
    clusterMaker                            html  
    cmdsplot                                html  
    controlQC                               html  
    countGC                                 html  
    cpgdensity                              html  
    dmrFdr                                  html  
    dmrFind                                 html  
    dmrFinder                               html  
    dmrPlot                                 html  
    getControlIndex                         html  
    maxDensity                              html  
    methPercent                             html  
    methp                                   html  
    normalizeBetweenSamples                 html  
    normalizeWithinSamples                  html  
    plotDMRs                                html  
    plotDensity                             html  
    plotRegions                             html  
    pmQuality                               html  
    qcReport                                html  
    qval                                    html  
    readCharm                               html  
    regionMatch                             html  
    regionPlot                              html  
    spatialAdjust                           html  
    validatePd                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'charm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'charm' as charm_2.28.0.zip
* DONE (charm)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'charm' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

charm.Rcheck/examples_i386/charm-Ex.timings

nameusersystemelapsed
bgAdjust000
clusterMaker000
cmdsplot000
controlQC000
cpgdensity5.080.335.41
dmrFind000
dmrFinder000
dmrPlot000
getControlIndex000
maxDensity0.030.000.04
methp000
normalizeWithinSamples000
plotDMRs000
plotDensity6.410.076.49
plotRegions000
pmQuality000
qval343.65 5.47349.14
readCharm000
regionMatch000
regionPlot000
spatialAdjust000
validatePd000

charm.Rcheck/examples_x64/charm-Ex.timings

nameusersystemelapsed
bgAdjust000
clusterMaker000
cmdsplot000
controlQC000
cpgdensity4.310.334.64
dmrFind000
dmrFinder000
dmrPlot000
getControlIndex000
maxDensity0.020.000.02
methp000
normalizeWithinSamples000
plotDMRs000
plotDensity5.000.085.08
plotRegions000
pmQuality000
qval341.47 4.89346.40
readCharm000
regionMatch000
regionPlot000
spatialAdjust000
validatePd000