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CHECK report for CGHbase on tokay2

This page was generated on 2018-10-17 08:33:51 -0400 (Wed, 17 Oct 2018).

Package 213/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.40.0
Mark van de Wiel
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CGHbase
Branch: RELEASE_3_7
Last Commit: a6cb7dc
Last Changed Date: 2018-04-30 10:35:09 -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: CGHbase
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CGHbase_1.40.0.tar.gz
StartedAt: 2018-10-17 01:00:26 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:01:22 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 56.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CGHbase.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:CGHbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CGHbase_1.40.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CGHbase.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 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' version '1.40.0'
* 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 'CGHbase' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:56: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:95: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:96: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:97: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:100: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:101: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:137: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:143: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:25: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:30: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:62: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:63: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:64: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:67: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:68: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:82: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:88: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:27: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:33: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:60: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:62: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:65: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:66: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:91: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CGHbase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'Biobase:::assayDataElement'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::assayDataDims'
  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
.makeEmptyFeatureData: no visible global function definition for 'is'
.makeEmptyFeatureData: no visible global function definition for 'new'
.makeEmptyFeatureDataForRegions: no visible global function definition
  for 'is'
.makeEmptyFeatureDataForRegions: no visible global function definition
  for 'new'
frequencyPlotCalls: no visible global function definition for 'rect'
frequencyPlotCalls: no visible global function definition for 'box'
frequencyPlotCalls: no visible global function definition for 'abline'
frequencyPlotCalls: no visible global function definition for 'axis'
frequencyPlotCalls: no visible global function definition for 'mtext'
frequencyPlotCalls: no visible global function definition for 'median'
make_cghRaw: no visible global function definition for 'read.table'
make_cghRaw: no visible global function definition for 'new'
summaryPlot: no visible global function definition for 'rect'
summaryPlot: no visible global function definition for 'box'
summaryPlot: no visible global function definition for 'abline'
summaryPlot: no visible global function definition for 'axis'
summaryPlot: no visible global function definition for 'mtext'
summaryPlot: no visible global function definition for 'median'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'par'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'barplot'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'segments'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'gray'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'box'
frequencyPlot,cghRegions-missing: no visible global function definition
  for 'axis'
initialize,cghCall: no visible global function definition for 'new'
initialize,cghCall: no visible global function definition for
  'callNextMethod'
initialize,cghRaw: no visible global function definition for 'new'
initialize,cghRaw: no visible global function definition for
  'callNextMethod'
initialize,cghRegions: no visible global function definition for 'new'
initialize,cghRegions: no visible global function definition for
  'callNextMethod'
initialize,cghSeg: no visible global function definition for 'new'
initialize,cghSeg: no visible global function definition for
  'callNextMethod'
plot.cghRegions,cghRegions-missing: no visible global function
  definition for 'layout'
plot.cghRegions,cghRegions-missing: no visible global function
  definition for 'par'
plot.cghRegions,cghRegions-missing: no visible global function
  definition for 'segments'
plot.cghRegions,cghRegions-missing: no visible global function
  definition for 'axis'
plot,cghCall-missing: no visible global function definition for 'par'
plot,cghCall-missing: no visible global function definition for 'rect'
plot,cghCall-missing: no visible global function definition for 'axis'
plot,cghCall-missing: no visible global function definition for 'box'
plot,cghCall-missing: no visible global function definition for
  'abline'
plot,cghCall-missing: no visible global function definition for 'mtext'
plot,cghCall-missing: no visible global function definition for 'title'
plot,cghCall-missing: no visible global function definition for
  'segments'
plot,cghCall-missing: no visible global function definition for
  'median'
plot,cghCall-missing : <anonymous>: no visible global function
  definition for 'mad'
plot,cghRaw-missing: no visible global function definition for 'mtext'
plot,cghRaw-missing: no visible global function definition for 'abline'
plot,cghRaw-missing: no visible global function definition for 'axis'
plot,cghRaw-missing: no visible global function definition for 'median'
plot,cghRaw-missing : <anonymous>: no visible global function
  definition for 'mad'
plot,cghSeg-missing: no visible global function definition for 'mtext'
plot,cghSeg-missing: no visible global function definition for 'abline'
plot,cghSeg-missing: no visible global function definition for 'axis'
plot,cghSeg-missing: no visible global function definition for
  'segments'
plot,cghSeg-missing: no visible global function definition for 'median'
plot,cghSeg-missing : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  abline axis barplot box callNextMethod gray is layout mad median
  mtext new par read.table rect segments title
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
             "mtext", "par", "rect", "segments", "title")
  importFrom("methods", "callNextMethod", "is", "new")
  importFrom("stats", "mad", "median")
  importFrom("utils", "read.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/CGHbase.Rcheck/00check.log'
for details.

Installation output

CGHbase.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/CGHbase_1.40.0.tar.gz && rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHbase.buildbin-libdir CGHbase_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CGHbase_1.40.0.zip && rm CGHbase_1.40.0.tar.gz CGHbase_1.40.0.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  848k  100  848k    0     0  14.8M      0 --:--:-- --:--:-- --:--:-- 17.2M

install for i386

* installing *source* package 'CGHbase' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CGHbase'
    finding HTML links ... done
    CGHbase-package                         html  
    Wilting                                 html  
    WiltingCalled                           html  
    WiltingNorm                             html  
    WiltingRaw                              html  
    WiltingRegions                          html  
    WiltingSeg                              html  
    avedist                                 html  
    chromosomes                             html  
    class.cghCall                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:42: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:56: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:95: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:96: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:97: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:100: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:101: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:137: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghCall.Rd:143: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    class.cghRaw                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:25: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:30: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:62: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:63: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:64: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:67: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:68: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:82: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghRaw.Rd:88: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    class.cghRegions                        html  
    class.cghSeg                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:27: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:33: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:60: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:62: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:65: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:66: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpY3tbQ0/R.INSTALL12a8572935d/CGHbase/man/class.cghSeg.Rd:91: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    copynumber                              html  
    frequencyPlot                           html  
    frequencyPlotCalls                      html  
    make_cghRaw                             html  
    plot                                    html  
    probloss                                html  
    regions                                 html  
    summaryPlot                             html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.40.0.zip
* DONE (CGHbase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CGHbase' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

CGHbase.Rcheck/examples_i386/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.090.000.09
class.cghRaw0.410.030.44
class.cghRegions0.230.000.23
class.cghSeg0.050.000.05
copynumber0.040.010.06
frequencyPlot000
frequencyPlotCalls0.020.000.01
make_cghRaw0.050.000.05
summaryPlot000

CGHbase.Rcheck/examples_x64/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.070.000.06
class.cghRaw0.280.000.28
class.cghRegions0.210.000.20
class.cghSeg0.030.000.03
copynumber0.030.000.03
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.060.000.07
summaryPlot000