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CHECK report for Neve2006 on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE Neve2006 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 249/385HostnameOS / ArchINSTALLBUILDCHECK
Neve2006 0.29.0
VJ Carey
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/Neve2006
Branch: master
Last Commit: 7f475e1
Last Changed Date: 2020-10-27 09:47:52 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: Neve2006
Version: 0.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Neve2006.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Neve2006_0.29.0.tar.gz
StartedAt: 2021-01-14 11:32:11 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:33:45 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 94.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Neve2006.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Neve2006.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Neve2006_0.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/Neve2006.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Neve2006/DESCRIPTION' ... OK
* this is package 'Neve2006' version '0.29.0'
* 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 'Neve2006' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 70.6Mb
  sub-directories of 1Mb or more:
    data     15.1Mb
    extdata  54.6Mb
* 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 ... 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:
  'Biobase' 'annotate' 'hgu133a.db' 'methods' 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
make_cghExSet: no visible global function definition for 'is'
make_cghExSet: no visible global function definition for 'new'
[,cghExSet: no visible global function definition for 'callNextMethod'
[,cghExSet: no visible global function definition for 'assayDataNew'
[,cghExSet: no visible global function definition for 'exprs'
[,cghExSet: no visible global function definition for 'phenoData'
initialize,cghExSet: no visible global function definition for 'new'
initialize,cghExSet: no visible global function definition for
  'callNextMethod'
initialize,cghExSet: no visible global function definition for
  'assayDataNew'
logRatios,cghExSet: no visible global function definition for
  'assayDataElement'
logRatios,cghSet: no visible global function definition for
  'assayDataElement'
show,cghExSet: no visible global function definition for 'storageMode'
show,cghExSet: no visible global function definition for 'selectSome'
show,cghExSet: no visible global function definition for 'featureNames'
show,cghExSet: no visible global function definition for 'dims'
show,cghExSet: no visible global function definition for 'show'
show,cghExSet: no visible global function definition for 'phenoData'
show,cghExSet: no visible global function definition for
  'experimentData'
show,cghExSet: no visible global function definition for 'annotation'
Undefined global functions or variables:
  annotation assayDataElement assayDataNew callNextMethod dims
  experimentData exprs featureNames is new phenoData selectSome show
  storageMode
Consider adding
  importFrom("methods", "callNextMethod", "is", "new", "show")
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 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/Neve2006.Rcheck/00check.log'
for details.



Installation output

Neve2006.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/Neve2006_0.29.0.tar.gz && rm -rf Neve2006.buildbin-libdir && mkdir Neve2006.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Neve2006.buildbin-libdir Neve2006_0.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Neve2006_0.29.0.zip && rm Neve2006_0.29.0.tar.gz Neve2006_0.29.0.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
 37 67.7M   37 25.5M    0     0  80.7M      0 --:--:-- --:--:-- --:--:-- 80.5M
100 67.7M  100 67.7M    0     0  94.9M      0 --:--:-- --:--:-- --:--:-- 94.8M

install for i386

* installing *source* package 'Neve2006' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Neve2006'
    finding HTML links ... done
    cghExSet-class                          html  
REDIRECT:topic	 cghExSet-class -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 [,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 cloneMeta,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 cloneNames,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 exprs,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 initialize,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 logRatios,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 show,cghExSet-method -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 cloneMeta -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 cloneNames -> cghExSet-class.html [ SUCCESS ]
REDIRECT:topic	 make_cghExSet -> cghExSet-class.html [ SUCCESS ]
    logRatios                               html  
REDIRECT:topic	 logRatios -> logRatios.html [ SUCCESS ]
REDIRECT:topic	 logRatios,cghSet-method -> logRatios.html [ SUCCESS ]
REDIRECT:topic	 cghSet-class -> logRatios.html [ SUCCESS ]
    neveCGHmatch                            html  
REDIRECT:topic	 neveCGHmatch -> neveCGHmatch.html [ SUCCESS ]
REDIRECT:topic	 neveRMAmatch -> neveCGHmatch.html [ SUCCESS ]
REDIRECT:topic	 neveExCGH -> neveCGHmatch.html [ SUCCESS ]
** 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 'Neve2006' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Neve2006' as Neve2006_0.29.0.zip
* DONE (Neve2006)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'Neve2006' successfully unpacked and MD5 sums checked

Tests output


Example timings

Neve2006.Rcheck/examples_i386/Neve2006-Ex.timings

nameusersystemelapsed
cghExSet-class0.640.050.69
logRatios0.040.000.04
neveCGHmatch0.660.050.70

Neve2006.Rcheck/examples_x64/Neve2006-Ex.timings

nameusersystemelapsed
cghExSet-class0.530.000.53
logRatios0.030.000.03
neveCGHmatch0.570.000.56