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This page was generated on 2022-01-18 11:07:06 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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 464/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 1.11.1  (landing page)
Francisco Jose Campos Laborie
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/deco
git_branch: master
git_last_commit: 97cb195
git_last_commit_date: 2021-11-20 23:30:43 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deco
Version: 1.11.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deco.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings deco_1.11.1.tar.gz
StartedAt: 2022-01-17 18:44:24 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 18:47:18 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 173.5 seconds
RetCode: 0
Status:   OK  
CheckDir: deco.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deco.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings deco_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/deco.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.11.1'
* 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
* 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 ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/deco.Rcheck/00check.log'
for details.



Installation output

deco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL deco
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (deco)
Making 'packages.html' ... done

Tests output


Example timings

deco.Rcheck/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.210.000.21
AnnotateDECO0.170.000.17
NSCAcluster0.910.641.55
deco-class0.020.000.02
deco-package0.170.020.18
decoNSCA0.170.030.21
decoRDA0.250.000.25
decoReport0.120.010.14
featureTable0.150.000.14
plotAssociationH2.670.032.72
plotDECOProfile0.110.020.12
plotGainingH1.140.011.17
plotHeatmapH0.140.040.17