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This page was generated on 2024-03-04 11:39:48 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1723/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGREAT 2.5.3  (landing page)
Zuguang Gu
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/rGREAT
git_branch: devel
git_last_commit: a8b2403
git_last_commit_date: 2024-02-05 08:42:06 -0500 (Mon, 05 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    OK    ERROR  

CHECK results for rGREAT on merida1


To the developers/maintainers of the rGREAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rGREAT.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: rGREAT
Version: 2.5.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rGREAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rGREAT_2.5.3.tar.gz
StartedAt: 2024-03-02 09:26:14 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 09:38:03 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 708.3 seconds
RetCode: 0
Status:   OK  
CheckDir: rGREAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rGREAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rGREAT_2.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rGREAT.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rGREAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGREAT’ version ‘2.5.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘BioMartGOGeneSets’
* 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 ‘rGREAT’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                               user system elapsed
plotRegionGeneAssociations-GreatObject-method 6.395  0.084   7.424
getRegionGeneAssociations-GreatObject-method  4.306  0.209   5.318
submitGreatJob                                0.772  0.084   7.432
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/rGREAT.Rcheck/00check.log’
for details.



Installation output

rGREAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rGREAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘rGREAT’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
make: Nothing to be done for `all'.
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-rGREAT/00new/rGREAT/libs
** R
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rGREAT)

Tests output

rGREAT.Rcheck/tests/test-all.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(rGREAT)))
> 
> test_check("rGREAT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 28.568   1.445  33.696 

Example timings

rGREAT.Rcheck/rGREAT-Ex.timings

nameusersystemelapsed
GreatJob-class0.0000.0000.001
GreatJob0.0010.0010.001
GreatObject-class0.0010.0000.001
GreatObject0.0000.0000.001
availableCategories-GreatJob-method0.1610.0120.203
availableOntologies-GreatJob-method0.1480.0090.178
extendTSS0.0000.0010.001
extendTSSFromDataFrame000
extendTSSFromOrgDb0.0010.0000.001
extendTSSFromTxDb0.0000.0000.001
getEnrichmentTable-GreatJob-method0.1620.0120.201
getEnrichmentTable-GreatObject-method0.1130.0170.149
getEnrichmentTable-dispatch0.0000.0000.001
getEnrichmentTables-GreatJob-method0.2900.0140.348
getEnrichmentTables-GreatObject-method0.0000.0010.001
getEnrichmentTables-dispatch0.0010.0000.001
getGREATDefaultTSS0.0000.0000.001
getGapFromUCSC0.1490.0050.186
getGeneSetsFromBioMart0.0000.0010.001
getGeneSetsFromOrgDb0.0000.0010.001
getGenesFromGencode0.0000.0010.000
getGenomeDataFromNCBI0.0000.0010.001
getKEGGGenome0.0000.0010.003
getKEGGPathways0.0010.0000.001
getRefSeqGenesFromUCSC0.0010.0010.001
getRegionGeneAssociations-GreatJob-method0.9240.0231.108
getRegionGeneAssociations-GreatObject-method4.3060.2095.318
getRegionGeneAssociations-dispatch0.0000.0000.001
getTSS000
great0.0010.0010.002
great_opt0.0340.0050.045
plotRegionGeneAssociationGraphs-GreatJob-method0.0000.0000.001
plotRegionGeneAssociations-GreatJob-method1.9750.1072.458
plotRegionGeneAssociations-GreatObject-method6.3950.0847.424
plotRegionGeneAssociations-dispatch000
plotVolcano-GreatJob-method0.0010.0010.001
plotVolcano-GreatObject-method0.0000.0010.000
plotVolcano-dispatch0.0000.0000.001
randomRegions0.5200.0380.648
randomRegionsFromBioMartGenome0.0000.0000.001
read_gmt0.0690.0993.746
reduce_by_start_and_end0.0000.0000.001
shinyReport-GreatJob-method0.0010.0000.001
shinyReport-GreatObject-method0.0000.0010.001
shinyReport-dispatch000
submitGreatJob0.7720.0847.432