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This page was generated on 2022-01-17 13:06:08 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for deco on tokay2


To the developers/maintainers of the deco package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deco.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 462/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 1.10.0  (landing page)
Francisco Jose Campos Laborie
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/deco
git_branch: RELEASE_3_14
git_last_commit: d18f24e
git_last_commit_date: 2021-10-26 12:48:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deco
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings deco_1.10.0.tar.gz
StartedAt: 2022-01-16 19:22:23 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:26:59 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 276.3 seconds
RetCode: 0
Status:   OK  
CheckDir: deco.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings deco_1.10.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/deco.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.10.0'
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.analysisType' '.heatplot.2'
* 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-3.14-bioc/meat/deco.Rcheck/00check.log'
for details.



Installation output

deco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/deco_1.10.0.tar.gz && rm -rf deco.buildbin-libdir && mkdir deco.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deco.buildbin-libdir deco_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL deco_1.10.0.zip && rm deco_1.10.0.tar.gz deco_1.10.0.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 2486k  100 2486k    0     0  5356k      0 --:--:-- --:--:-- --:--:-- 5370k

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_1.10.0.zip
* DONE (deco)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'deco' successfully unpacked and MD5 sums checked

Tests output


Example timings

deco.Rcheck/examples_i386/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.340.030.38
AnnotateDECO0.190.020.20
NSCAcluster1.450.291.75
deco-class000
deco-package0.320.000.33
decoNSCA0.270.020.28
decoRDA0.250.000.25
decoReport0.220.000.22
featureTable0.220.000.22
plotAssociationH3.470.193.65
plotDECOProfile0.200.010.22
plotGainingH1.300.021.31
plotHeatmapH0.220.010.24

deco.Rcheck/examples_x64/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.280.000.28
AnnotateDECO0.150.020.17
NSCAcluster1.000.441.44
deco-class000
deco-package0.300.000.29
decoNSCA0.170.030.21
decoRDA0.170.010.18
decoReport0.160.020.17
featureTable0.170.000.18
plotAssociationH2.750.052.79
plotDECOProfile0.140.010.16
plotGainingH1.610.051.66
plotHeatmapH0.290.010.31