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CHECK report for LiquidAssociation on malbec2

This page was generated on 2020-10-17 11:55:02 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE LiquidAssociation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 944/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LiquidAssociation 1.42.0
Yen-Yi Ho
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/LiquidAssociation
Branch: RELEASE_3_11
Last Commit: 8e34c85
Last Changed Date: 2020-04-27 14:20:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LiquidAssociation
Version: 1.42.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings LiquidAssociation_1.42.0.tar.gz
StartedAt: 2020-10-17 02:39:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:41:16 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 96.0 seconds
RetCode: 0
Status:  OK 
CheckDir: LiquidAssociation.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings LiquidAssociation_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/LiquidAssociation.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘LiquidAssociation’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘geepack’ ‘org.Sc.sgd.db’ ‘yeastCC’
  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
CNM.full,matrix: no visible global function definition for ‘geese’
CNM.full,matrix: no visible binding for global variable ‘groupid’
CNM.full,matrix: no visible binding for global variable ‘visit’
CNM.full,matrix: no visible global function definition for
  ‘geese.control’
CNM.simple,matrix: no visible global function definition for ‘geese’
CNM.simple,matrix: no visible binding for global variable ‘groupid’
CNM.simple,matrix: no visible binding for global variable ‘visit’
CNM.simple,matrix: no visible global function definition for
  ‘geese.control’
Undefined global functions or variables:
  geese geese.control groupid visit
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getsGLA-methods 5.813  0.047   5.862
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.



Installation output

LiquidAssociation.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL LiquidAssociation
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘LiquidAssociation’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (LiquidAssociation)

Tests output


Example timings

LiquidAssociation.Rcheck/LiquidAssociation-Ex.timings

nameusersystemelapsed
CNM-class0.0020.0000.002
CNM.full-methods0.0330.0040.073
CNM.simple-methods0.0180.0000.018
GLA-methods0.0040.0030.007
LA-methods0.0020.0000.002
LiquidAssociation-package0.1360.0000.136
getsGLA-methods5.8130.0475.862
getsLA-methods2.7660.0122.778
plotGLA-methods0.0320.0001.034