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This page was generated on 2024-02-22 12:48:11 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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

Package 1093/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LiquidAssociation 1.57.0  (landing page)
Yen-Yi Ho
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/LiquidAssociation
git_branch: devel
git_last_commit: 5adc752
git_last_commit_date: 2023-10-24 09:42:56 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for LiquidAssociation on nebbiolo1


To the developers/maintainers of the LiquidAssociation package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: LiquidAssociation
Version: 1.57.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings LiquidAssociation_1.57.0.tar.gz
StartedAt: 2024-02-22 00:08:09 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 00:10:04 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 114.6 seconds
RetCode: 0
Status:   OK  
CheckDir: LiquidAssociation.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:LiquidAssociation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings LiquidAssociation_1.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/LiquidAssociation.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ version ‘1.57.0’
* 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 loading without being on the library search path ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.



Installation output

LiquidAssociation.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL LiquidAssociation
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-class0.0010.0000.001
CNM.full-methods0.1360.0000.136
CNM.simple-methods0.0120.0000.012
GLA-methods0.0050.0000.005
LA-methods0.0020.0000.001
LiquidAssociation-package0.0630.0000.062
getsGLA-methods3.8810.1244.006
getsLA-methods2.1790.0042.182
plotGLA-methods0.0230.0001.024