Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:36:37 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for enrichTF on palomino4


To the developers/maintainers of the enrichTF package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/enrichTF.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: enrichTF
Version: 1.18.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:enrichTF.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings enrichTF_1.18.0.tar.gz
StartedAt: 2024-03-26 00:36:31 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:45:35 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 544.1 seconds
RetCode: 0
Status:   OK  
CheckDir: enrichTF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:enrichTF.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings enrichTF_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/enrichTF.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
TissueOpennessSpecificity 25.23   0.18   25.44
GeneOntology              18.06   1.44   19.53
GenBackground              6.25   2.14   36.18
Pipelines                  1.70   0.24   21.31
MotifsInRegions            0.93   0.09   21.75
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/enrichTF.Rcheck/00check.log'
for details.



Installation output

enrichTF.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL enrichTF
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:02 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:03 EDT"
[1] "2024-03-26 00:45:24 EDT"
[1] "2024-03-26 00:45:24 EDT"
[1] "2024-03-26 00:45:24 EDT"
[1] "2024-03-26 00:45:24 EDT"
[1] "2024-03-26 00:45:24 EDT"
[1] "2024-03-26 00:45:24 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  25.10    3.10   49.56 

Example timings

enrichTF.Rcheck/enrichTF-Ex.timings

nameusersystemelapsed
GenBackground 6.25 2.1436.18
GeneOntology18.06 1.4419.53
MotifsInRegions 0.93 0.0921.75
Pipelines 1.70 0.2421.31
RegionConnectTargetGene0.490.120.63
TFsEnrichInRegions0.670.310.99
TissueOpennessConserve0.180.030.22
TissueOpennessSpecificity25.23 0.1825.44
UnzipAndMergeBed0.110.060.88