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CHECK report for arrayMvout on riesling1

This page was generated on 2020-10-28 13:27:43 -0400 (Wed, 28 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE arrayMvout PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 83/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayMvout 1.48.0
V. Carey
Snapshot Date: 2020-10-27 13:12:07 -0400 (Tue, 27 Oct 2020)
URL: https://git.bioconductor.org/packages/arrayMvout
Branch: RELEASE_3_12
Last Commit: 3d9d8e4
Last Changed Date: 2020-10-27 10:34:44 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: arrayMvout
Version: 1.48.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:arrayMvout.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings arrayMvout_1.48.0.tar.gz
StartedAt: 2020-10-27 20:04:35 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 20:12:22 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 466.7 seconds
RetCode: 0
Status:  OK  
CheckDir: arrayMvout.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:arrayMvout.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings arrayMvout_1.48.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/arrayMvout.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 'arrayMvout/DESCRIPTION' ... OK
* this is package 'arrayMvout' version '1.48.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'arrayMvout' can be installed ... OK
* checking installed package size ... OK
* 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' 'affy' 'lumi' 'methods' 'parody'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.affyArrayOutliers: no visible global function definition for
  'sampleNames'
.affyArrayOutliers: no visible global function definition for 'fitPLM'
.affyArrayOutliers: no visible global function definition for 'boxplot'
.affyArrayOutliers: no visible global function definition for 'Mbox'
.affyArrayOutliers: no visible global function definition for
  'AffyRNAdeg'
.affyArrayOutliers: no visible global function definition for 'prcomp'
.affyArrayOutliers : <anonymous>: no visible global function definition
  for 'mv.calout.detect'
.affyArrayOutliers: no visible global function definition for
  'mv.calout.detect'
.lumiArrayOutliers: no visible global function definition for 'lumiQ'
.lumiArrayOutliers: no visible global function definition for 'prcomp'
.lumiArrayOutliers: no visible global function definition for
  'mv.calout.detect'
.lumiArrayOutliers : <anonymous>: no visible global function definition
  for 'mv.calout.detect'
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for 'prcomp'
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for 'mv.calout.detect'
ArrayOutliers,data.frame-numeric-ANY : <anonymous>: no visible global
  function definition for 'mv.calout.detect'
plot,arrOutStruct-ANY: no visible global function definition for
  'biplot'
plot,arrOutStruct-ANY: no visible global function definition for
  'prcomp'
Undefined global functions or variables:
  AffyRNAdeg Mbox biplot boxplot fitPLM lumiQ mv.calout.detect prcomp
  sampleNames
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "biplot", "prcomp")
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 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
ArrayOutliers-methods 15.28   0.27   15.66
ArrayOutliers         14.37   0.12   14.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
ArrayOutliers-methods 13.66   0.29   13.95
ArrayOutliers         10.99   0.25   11.23
* 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-3.12-bioc/meat/arrayMvout.Rcheck/00check.log'
for details.



Installation output

arrayMvout.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/arrayMvout_1.48.0.tar.gz && rm -rf arrayMvout.buildbin-libdir && mkdir arrayMvout.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=arrayMvout.buildbin-libdir arrayMvout_1.48.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL arrayMvout_1.48.0.zip && rm arrayMvout_1.48.0.tar.gz arrayMvout_1.48.0.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
100  297k  100  297k    0     0  2158k      0 --:--:-- --:--:-- --:--:-- 2174k

install for i386

* installing *source* package 'arrayMvout' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** help
*** installing help indices
  converting help for package 'arrayMvout'
    finding HTML links ... done
    ArrayOutliers-methods                   html  
    ArrayOutliers                           html  
    arrOutStruct-class                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'arrayMvout' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'arrayMvout' as arrayMvout_1.48.0.zip
* DONE (arrayMvout)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'arrayMvout' successfully unpacked and MD5 sums checked

Tests output


Example timings

arrayMvout.Rcheck/examples_i386/arrayMvout-Ex.timings

nameusersystemelapsed
ArrayOutliers-methods15.28 0.2715.66
ArrayOutliers14.37 0.1214.50
arrOutStruct-class0.060.000.06

arrayMvout.Rcheck/examples_x64/arrayMvout-Ex.timings

nameusersystemelapsed
ArrayOutliers-methods13.66 0.2913.95
ArrayOutliers10.99 0.2511.23
arrOutStruct-class0.030.000.03