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This page was generated on 2023-03-18 11:06:08 -0400 (Sat, 18 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4282
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4279
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4145
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 LiquidAssociation on merida1


To the developers/maintainers of the LiquidAssociation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LiquidAssociation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1055/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LiquidAssociation 1.53.0  (landing page)
Yen-Yi Ho
Snapshot Date: 2023-03-17 14:27:35 -0400 (Fri, 17 Mar 2023)
git_url: https://git.bioconductor.org/packages/LiquidAssociation
git_branch: master
git_last_commit: 280d237
git_last_commit_date: 2022-11-01 11:04:45 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: LiquidAssociation
Version: 1.53.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LiquidAssociation_1.53.0.tar.gz
StartedAt: 2023-03-18 02:22:21 -0400 (Sat, 18 Mar 2023)
EndedAt: 2023-03-18 02:27:03 -0400 (Sat, 18 Mar 2023)
EllapsedTime: 282.7 seconds
RetCode: 0
Status:   OK  
CheckDir: LiquidAssociation.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LiquidAssociation_1.53.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/LiquidAssociation.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ version ‘1.53.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getsGLA-methods 9.263  0.180  12.828
getsLA-methods  5.856  0.032   8.014
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.



Installation output

LiquidAssociation.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LiquidAssociation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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-methods0.0760.0030.142
CNM.simple-methods0.0490.0000.066
GLA-methods0.0080.0000.013
LA-methods0.0030.0010.002
LiquidAssociation-package0.1860.0010.256
getsGLA-methods 9.263 0.18012.828
getsLA-methods5.8560.0328.014
plotGLA-methods0.0460.0011.056