Back to Multiple platform build/check report for BioC 3.13 experimental data
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

CHECK report for HD2013SGI on riesling1

This page was generated on 2021-01-14 15:59:08 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HD2013SGI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 163/385HostnameOS / ArchINSTALLBUILDCHECK
HD2013SGI 1.31.0
Bernd Fischer
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/HD2013SGI
Branch: master
Last Commit: 8971f18
Last Changed Date: 2020-10-27 10:01:22 -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: HD2013SGI
Version: 1.31.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HD2013SGI.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz
StartedAt: 2021-01-14 11:22:31 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:26:30 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 239.0 seconds
RetCode: 0
Status:  OK  
CheckDir: HD2013SGI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HD2013SGI.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/HD2013SGI.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 'HD2013SGI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HD2013SGI' version '1.31.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RColorBrewer', 'gplots', 'geneplotter', 'splots', 'limma', 'vcd',
  'LSD', 'EBImage'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'HD2013SGI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 525.3Mb
  sub-directories of 1Mb or more:
    data  524.1Mb
* 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
Packages in Depends field not imported from:
  'EBImage' 'LSD' 'RColorBrewer' 'geneplotter' 'gplots' 'limma'
  'splots' 'vcd'
  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:
  'humanReadableNames'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for 'unit'
HD2013SGIHeatmapHuman: no visible global function definition for
  'pushViewport'
HD2013SGIHeatmapHuman: no visible global function definition for
  'viewport'
HD2013SGIHeatmapHuman: no visible global function definition for
  'grid.layout'
HD2013SGIHeatmapHuman: no visible global function definition for
  'grid.rect'
HD2013SGIHeatmapHuman: no visible global function definition for
  'grid.raster'
HD2013SGIHeatmapHuman: no visible global function definition for
  'popViewport'
HD2013SGIHeatmapHuman: no visible global function definition for
  'grid.text'
HD2013SGIHeatmapHuman: no visible global function definition for 'gpar'
HD2013SGImaineffects: no visible binding for global variable 'median'
HD2013SGImaineffects : <anonymous>: no visible binding for global
  variable 'median'
HD2013SGImaineffects: no visible global function definition for
  'median'
HD2013SGIorderDim: no visible global function definition for 'cor'
HD2013SGIorderDim: no visible global function definition for 'hclust'
HD2013SGIorderDim: no visible global function definition for 'as.dist'
HD2013SGIselectByStability: no visible global function definition for
  'lm'
HD2013SGIselectByStability : <anonymous>: no visible global function
  definition for 'cor'
plotExampleInteractions: no visible binding for global variable 'sd'
plotExampleInteractions: no visible global function definition for
  'par'
plotExampleInteractions: no visible global function definition for
  'barplot'
plotExampleInteractions: no visible global function definition for
  'abline'
plotExampleInteractions: no visible global function definition for
  'points'
plotExampleInteractions: no visible global function definition for
  'text'
plotExampleSingleGeneEffects: no visible global function definition for
  'mad'
plotExampleSingleGeneEffects: no visible global function definition for
  'par'
plotExampleSingleGeneEffects: no visible global function definition for
  'barplot'
plotExampleSingleGeneEffects: no visible global function definition for
  'abline'
plotExampleSingleGeneEffects: no visible global function definition for
  'points'
Undefined global functions or variables:
  abline as.dist barplot cor gpar grid.layout grid.raster grid.rect
  grid.text hclust lm mad median par points popViewport pushViewport sd
  text unit viewport
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad", "median",
             "sd")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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
featuresPerWell 37.88   0.50   38.37
datamatrixfull   8.43   0.11    8.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
featuresPerWell 29.35   0.45   29.81
datamatrixfull   6.60   0.11    6.71
* 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/HD2013SGI.Rcheck/00check.log'
for details.



Installation output

HD2013SGI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/HD2013SGI_1.31.0.tar.gz && rm -rf HD2013SGI.buildbin-libdir && mkdir HD2013SGI.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HD2013SGI.buildbin-libdir HD2013SGI_1.31.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HD2013SGI_1.31.0.zip && rm HD2013SGI_1.31.0.tar.gz HD2013SGI_1.31.0.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
 10  524M   10 54.2M    0     0  61.6M      0  0:00:08 --:--:--  0:00:08 61.6M
 30  524M   30  157M    0     0  85.1M      0  0:00:06  0:00:01  0:00:05 85.1M
 48  524M   48  255M    0     0  78.8M      0  0:00:06  0:00:03  0:00:03 78.8M
 62  524M   62  327M    0     0  84.8M      0  0:00:06  0:00:03  0:00:03 84.8M
 83  524M   83  438M    0     0  90.3M      0  0:00:05  0:00:04  0:00:01 90.3M
100  524M  100  524M    0     0  92.9M      0  0:00:05  0:00:05 --:--:-- 98.7M

install for i386

* installing *source* package 'HD2013SGI' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HD2013SGI'
    finding HTML links ... done
    HD2013SGI-package                       html  
REDIRECT:topic	 HD2013SGI-package -> HD2013SGI-package.html [ SUCCESS ]
REDIRECT:topic	 HD2013SGI -> HD2013SGI-package.html [ SUCCESS ]
    HD2013SGIHeatmapHuman                   html  
REDIRECT:topic	 HD2013SGIHeatmapHuman -> HD2013SGIHeatmapHuman.html [ SUCCESS ]
    HD2013SGImaineffects                    html  
REDIRECT:topic	 HD2013SGImaineffects -> HD2013SGImaineffects.html [ SUCCESS ]
    HD2013SGIorderDim                       html  
REDIRECT:topic	 HD2013SGIorderDim -> HD2013SGIorderDim.html [ SUCCESS ]
    HD2013SGIselectByStability              html  
REDIRECT:topic	 HD2013SGIselectByStability -> HD2013SGIselectByStability.html [ SUCCESS ]
    Interactions                            html  
REDIRECT:topic	 Interactions -> Interactions.html [ SUCCESS ]
    QueryAnnotation                         html  
REDIRECT:topic	 QueryAnnotation -> QueryAnnotation.html [ SUCCESS ]
    TargetAnnotation                        html  
REDIRECT:topic	 TargetAnnotation -> TargetAnnotation.html [ SUCCESS ]
    datamatrix                              html  
REDIRECT:topic	 datamatrix -> datamatrix.html [ SUCCESS ]
    datamatrixfull                          html  
REDIRECT:topic	 datamatrixfull -> datamatrixfull.html [ SUCCESS ]
    featuresPerWell                         html  
REDIRECT:topic	 featuresPerWell -> featuresPerWell.html [ SUCCESS ]
    mainEffects                             html  
REDIRECT:topic	 mainEffects -> mainEffects.html [ SUCCESS ]
    nrOfInteractionsPerTarget               html  
REDIRECT:topic	 nrOfInteractionsPerTarget -> nrOfInteractionsPerTarget.html [ SUCCESS ]
    stabilitySelection                      html  
REDIRECT:topic	 stabilitySelection -> stabilitySelection.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 'HD2013SGI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HD2013SGI' as HD2013SGI_1.31.0.zip
* DONE (HD2013SGI)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'HD2013SGI' successfully unpacked and MD5 sums checked

Tests output


Example timings

HD2013SGI.Rcheck/examples_i386/HD2013SGI-Ex.timings

nameusersystemelapsed
HD2013SGI-package0.030.010.04
Interactions0.050.000.05
QueryAnnotation000
TargetAnnotation0.020.000.01
datamatrix0.050.000.05
datamatrixfull8.430.118.57
featuresPerWell37.88 0.5038.37
mainEffects0.250.000.27
nrOfInteractionsPerTarget0.000.000.01
stabilitySelection0.020.020.03

HD2013SGI.Rcheck/examples_x64/HD2013SGI-Ex.timings

nameusersystemelapsed
HD2013SGI-package0.050.000.05
Interactions0.030.000.04
QueryAnnotation000
TargetAnnotation0.000.010.02
datamatrix0.050.000.04
datamatrixfull6.600.116.71
featuresPerWell29.35 0.4529.81
mainEffects0.240.020.25
nrOfInteractionsPerTarget0.010.000.02
stabilitySelection0.000.000.01