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CHECK report for cghMCR on riesling1

This page was generated on 2020-10-24 11:04:46 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cghMCR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 270/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cghMCR 1.47.0
J. Zhang
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/cghMCR
Branch: master
Last Commit: ac6f1bb
Last Changed Date: 2020-04-27 14:13:14 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cghMCR
Version: 1.47.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cghMCR_1.47.0.tar.gz
StartedAt: 2020-10-24 01:55:34 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 01:59:08 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 213.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cghMCR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cghMCR_1.47.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/cghMCR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.47.0'
* 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 'cghMCR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 98.2Mb
  sub-directories of 1Mb or more:
    sampleData  97.1Mb
* 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 'DNAcopy' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'CNTools' 'DNAcopy' 'limma' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'adjustSegments' 'alignGenes' 'drawSegs' 'getAdjustments'
  'highlightChrom' 'markChrom'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.DNAcopy
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SGOL: no visible global function definition for 'segBy'
SGOL: no visible global function definition for 'rs'
drawSegs : drawSegLine: no visible global function definition for
  'lines'
dropGenes: no visible global function definition for 'approx'
getAlteredSegs: no visible global function definition for 'quantile'
getLineData: no visible global function definition for 'median'
getSegData: no visible global function definition for 'read.maimages'
getSegData: no visible global function definition for
  'normalizeWithinArrays'
getSegData: no visible global function definition for
  'backgroundCorrect'
getSegData: no visible global function definition for 'CNA'
getSegData: no visible global function definition for 'segment'
getSegData: no visible global function definition for 'smooth.CNA'
highlightChrom: no visible global function definition for 'polygon'
markChrom: no visible global function definition for 'polygon'
plot.DNAcopy: no visible global function definition for 'png'
plot.DNAcopy: no visible global function definition for 'par'
plot.DNAcopy: no visible global function definition for 'axis'
plot.DNAcopy: no visible global function definition for 'box'
plot.DNAcopy: no visible global function definition for 'points'
plot.DNAcopy: no visible global function definition for 'lines'
plot.DNAcopy: no visible global function definition for 'dev.off'
plot.MCR: no visible global function definition for 'png'
plot.MCR: no visible global function definition for 'par'
plot.MCR: no visible global function definition for 'dev.off'
plotSGOL: no visible global function definition for 'lines'
plotSGOL: no visible global function definition for 'axis'
plotSGOL: no visible global function definition for 'box'
showMCR : <anonymous>: no visible global function definition for
  'median'
showMCR: no visible global function definition for 'lines'
showMCR: no visible global function definition for 'median'
showSegment : getMean: no visible global function definition for
  'median'
topGenes: no visible global function definition for 'quantile'
Undefined global functions or variables:
  CNA approx axis backgroundCorrect box dev.off lines median
  normalizeWithinArrays par png points polygon quantile read.maimages
  rs segBy segment smooth.CNA
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "box", "lines", "par", "points",
             "polygon")
  importFrom("stats", "approx", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'SGOL,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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, 4 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/cghMCR.Rcheck/00check.log'
for details.



Installation output

cghMCR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/cghMCR_1.47.0.tar.gz && rm -rf cghMCR.buildbin-libdir && mkdir cghMCR.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cghMCR.buildbin-libdir cghMCR_1.47.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL cghMCR_1.47.0.zip && rm cghMCR_1.47.0.tar.gz cghMCR_1.47.0.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
 22 36.5M   22 8427k    0     0  21.0M      0  0:00:01 --:--:--  0:00:01 20.9M
100 36.5M  100 36.5M    0     0  52.5M      0 --:--:-- --:--:-- --:--:-- 52.4M

install for i386

* installing *source* package 'cghMCR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cghMCR'
    finding HTML links ... done
    SGOL-class                              html  
    cghMCR-class                            html  
    cghMCR                                  html  
    mergeMCRProbes                          html  
    methods                                 html  
    plot.DNAcopy                            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 'cghMCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cghMCR' as cghMCR_1.47.0.zip
* DONE (cghMCR)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'cghMCR' successfully unpacked and MD5 sums checked

Tests output


Example timings

cghMCR.Rcheck/examples_i386/cghMCR-Ex.timings

nameusersystemelapsed
SGOL-class000
cghMCR-class0.080.000.08
cghMCR0.020.000.02
mergeMCRProbes2.70.02.7
plot.DNAcopy000

cghMCR.Rcheck/examples_x64/cghMCR-Ex.timings

nameusersystemelapsed
SGOL-class000
cghMCR-class0.060.000.06
cghMCR000
mergeMCRProbes3.110.033.15
plot.DNAcopy000