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This page was generated on 2022-01-19 06:00:08 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
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 PANTHER.db on nebbiolo2


To the developers/maintainers of the PANTHER.db package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 27/33HostnameOS / ArchINSTALLBUILDCHECK
PANTHER.db 1.0.10  (landing page)
Julius Muller
Snapshot Date: 2022-01-19 02:30:01 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/PANTHER.db
git_branch: master
git_last_commit: 191928c
git_last_commit_date: 2021-03-05 12:46:43 -0500 (Fri, 05 Mar 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  NO, version to propagate (1.0.10) is lower than published version (1.0.11)

Summary

Package: PANTHER.db
Version: 1.0.10
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PANTHER.db.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PANTHER.db_1.0.10.tar.gz
StartedAt: 2022-01-19 03:02:42 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 03:04:40 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 118.4 seconds
RetCode: 0
Status:   OK  
CheckDir: PANTHER.db.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PANTHER.db.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PANTHER.db_1.0.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-annotation/meat/PANTHER.db.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PANTHER.db/DESCRIPTION’ ... OK
* this is package ‘PANTHER.db’ version ‘1.0.10’
* 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 ‘PANTHER.db’ 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘PANTHER.db_unit_tests.R’
 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: OK


Installation output

PANTHER.db.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PANTHER.db
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘PANTHER.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PANTHER.db.Rmd’ using ‘UTF-8’ 
** 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 (PANTHER.db)

Tests output

PANTHER.db.Rcheck/tests/PANTHER.db_unit_tests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

> 
> requireNamespace("PANTHER.db") || stop("unable to load PANTHER.db")
Loading required namespace: PANTHER.db
[1] TRUE
> PANTHER.db:::.test()
Loading required package: PANTHER.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

Loading required package: RSQLite
PANTHER.db version 1.0.10


RUNIT TEST PROTOCOL -- Wed Jan 19 03:04:38 2022 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PANTHER.db RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  6.603   0.397   8.084 

Example timings

PANTHER.db.Rcheck/PANTHER.db-Ex.timings

nameusersystemelapsed
PANTHERDB-class3.2400.1934.122