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This page was generated on 2021-10-21 12:04:40 -0400 (Thu, 21 Oct 2021).

CHECK results for CGHbase on riesling1

To the developers/maintainers of the CGHbase package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGHbase.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 283/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.53.0  (landing page)
Mark van de Wiel
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/CGHbase
git_branch: master
git_last_commit: a8d3c92
git_last_commit_date: 2021-05-19 11:40:57 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CGHbase
Version: 1.53.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHbase.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CGHbase_1.53.0.tar.gz
StartedAt: 2021-10-21 00:50:55 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 00:54:39 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 223.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHbase.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CGHbase_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/CGHbase.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.53.0'
* 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 ... OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.14-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 http://155.52.207.166/BBS/3.14/bioc/src/contrib/CGHbase_1.53.0.tar.gz && rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHbase.buildbin-libdir CGHbase_1.53.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CGHbase_1.53.0.zip && rm CGHbase_1.53.0.tar.gz CGHbase_1.53.0.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
 42  849k   42  358k    0     0  1198k      0 --:--:-- --:--:-- --:--:-- 1198k
100  849k  100  849k    0     0  1756k      0 --:--:-- --:--:-- --:--:-- 1752k

install for i386

* installing *source* package 'CGHbase' ...
** using staged installation
** 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  
    class.cghRaw                            html  
    class.cghRegions                        html  
    class.cghSeg                            html  
    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 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 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.53.0.zip
* DONE (CGHbase)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'CGHbase' successfully unpacked and MD5 sums checked

Tests output


Example timings

CGHbase.Rcheck/examples_i386/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.030.000.03
class.cghRaw0.210.000.20
class.cghRegions0.130.000.12
class.cghSeg0.010.000.02
copynumber0.030.000.03
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.050.000.05
summaryPlot000

CGHbase.Rcheck/examples_x64/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.040.000.04
class.cghRaw0.210.020.22
class.cghRegions0.140.000.14
class.cghSeg0.010.000.02
copynumber0.030.000.03
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.030.000.03
summaryPlot000