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This page was generated on 2024-04-18 11:32:09 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 643/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
enrichTF 1.18.0  (landing page)
Zheng Wei
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/enrichTF
git_branch: RELEASE_3_18
git_last_commit: fab8b47
git_last_commit_date: 2023-10-24 11:13:36 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'motifmatchr' which is only available as a source package that needs compilation

CHECK results for enrichTF on kjohnson1


To the developers/maintainers of the enrichTF package:
- 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: enrichTF
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enrichTF_1.18.0.tar.gz
StartedAt: 2024-04-17 12:53:26 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 13:01:32 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 485.8 seconds
RetCode: 0
Status:   OK  
CheckDir: enrichTF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings enrichTF_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/enrichTF.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘enrichTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichTF’ version ‘1.18.0’
* package encoding: UTF-8
* 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 ‘enrichTF’ 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 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 ... NOTE
processing,TissueOpennessConserve: no visible global function
  definition for ‘as’
processing,TissueOpennessConserve: no visible binding for global
  variable ‘X2’
processing,TissueOpennessSpecificity: no visible global function
  definition for ‘as’
Undefined global functions or variables:
  X2 as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
GeneOntology              20.837  1.284  22.236
TissueOpennessSpecificity 20.085  0.241  20.382
GenBackground              4.857  0.650   5.631
Pipelines                  1.417  0.264  21.488
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/enrichTF.Rcheck/00check.log’
for details.



Installation output

enrichTF.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘enrichTF’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (enrichTF)

Tests output

enrichTF.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> library(testthat)
> library(enrichTF)
Loading required package: pipeFrame

> 
> test_check("enrichTF")
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:17 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:18 EDT"
[1] "2024-04-17 13:01:20 EDT"
[1] "2024-04-17 13:01:20 EDT"
[1] "2024-04-17 13:01:20 EDT"
[1] "2024-04-17 13:01:20 EDT"
[1] "2024-04-17 13:01:20 EDT"
[1] "2024-04-17 13:01:20 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 25.675   2.466  27.783 

Example timings

enrichTF.Rcheck/enrichTF-Ex.timings

nameusersystemelapsed
GenBackground4.8570.6505.631
GeneOntology20.837 1.28422.236
MotifsInRegions1.7600.8952.039
Pipelines 1.417 0.26421.488
RegionConnectTargetGene0.6090.0770.722
TFsEnrichInRegions0.5850.0770.664
TissueOpennessConserve0.1260.0130.139
TissueOpennessSpecificity20.085 0.24120.382
UnzipAndMergeBed0.0870.0120.100