Back to Multiple platform build/check report for BioC 3.12
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for deco on tokay1

This page was generated on 2021-05-06 12:30:37 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the deco package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 437/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 1.6.0  (landing page)
Francisco Jose Campos Laborie
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/deco
Branch: RELEASE_3_12
Last Commit: 910e12a
Last Changed Date: 2020-10-27 11:41:19 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: deco
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings deco_1.6.0.tar.gz
StartedAt: 2021-05-06 02:01:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:06:24 -0400 (Thu, 06 May 2021)
EllapsedTime: 300.2 seconds
RetCode: 0
Status:   OK   
CheckDir: deco.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings deco_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/deco.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'deco/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deco' version '1.6.0'
* 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 'deco' can be installed ... OK
* checking installed package size ... OK
* 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
Missing or unexported object: 'made4::array2ade4'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotAssociationH: no visible binding for global variable 'Subclasses'
plotAssociationH: no visible binding for global variable 'h.statistic'
plotAssociationH: no visible binding for global variable 'input.info'
plotAssociationH: no visible binding for global variable
  'DECO.subclasses'
plotAssociationH: no visible binding for global variable 'Samples'
plotAssociationH: no visible binding for global variable 'Features'
plotGainingH: no visible binding for global variable 'omic.data'
plotGainingH: no visible binding for global variable 'h.statistic'
plotGainingH: no visible binding for global variable 'ranking'
Undefined global functions or variables:
  DECO.subclasses Features Samples Subclasses h.statistic input.info
  omic.data ranking
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/deco.Rcheck/00check.log'
for details.



Installation output

deco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/deco_1.6.0.tar.gz && rm -rf deco.buildbin-libdir && mkdir deco.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deco.buildbin-libdir deco_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL deco_1.6.0.zip && rm deco_1.6.0.tar.gz deco_1.6.0.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
100 2488k  100 2488k    0     0  8181k      0 --:--:-- --:--:-- --:--:-- 8213k

install for i386

* installing *source* package 'deco' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deco'
    finding HTML links ... done
    ALCLdata                                html  
    AnnotateDECO                            html  
    NSCAcluster                             html  
    deco-class                              html  
    deco-package                            html  
    decoNSCA                                html  
    decoRDA                                 html  
    decoReport                              html  
    featureTable                            html  
    plotAssociationH                        html  
    plotDECOProfile                         html  
    plotGainingH                            html  
    plotHeatmapH                            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 'deco' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deco' as deco_1.6.0.zip
* DONE (deco)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'deco' successfully unpacked and MD5 sums checked

Tests output


Example timings

deco.Rcheck/examples_i386/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.280.070.36
AnnotateDECO0.170.020.19
NSCAcluster0.970.311.28
deco-class000
deco-package0.220.020.24
decoNSCA0.250.000.25
decoRDA0.190.050.23
decoReport0.220.000.22
featureTable0.180.000.19
plotAssociationH2.800.012.82
plotDECOProfile0.180.020.20
plotGainingH1.220.031.25
plotHeatmapH0.210.000.20

deco.Rcheck/examples_x64/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.360.000.36
AnnotateDECO0.250.000.25
NSCAcluster1.230.311.55
deco-class000
deco-package0.200.020.22
decoNSCA0.160.030.18
decoRDA0.170.020.19
decoReport0.160.000.16
featureTable0.150.000.15
plotAssociationH4.210.014.22
plotDECOProfile0.200.020.22
plotGainingH1.420.011.44
plotHeatmapH0.160.000.16