Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:06:04 -0400 (Fri, 17 Sep 2021).

CHECK results for enrichTF on tokay2

To the developers/maintainers of the enrichTF package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 575/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
enrichTF 1.8.0  (landing page)
Zheng Wei
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/enrichTF
git_branch: RELEASE_3_13
git_last_commit: 956c94b
git_last_commit_date: 2021-05-19 12:43:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: enrichTF
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:enrichTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings enrichTF_1.8.0.tar.gz
StartedAt: 2021-09-16 22:47:11 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:58:35 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 683.5 seconds
RetCode: 0
Status:   OK  
CheckDir: enrichTF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:enrichTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings enrichTF_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'enrichTF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'enrichTF' version '1.8.0'
* 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
* loading checks for arch 'i386'
** 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
processing,TissueOpennessConserve: no visible binding for global
  variable 'X2'
Undefined global functions or variables:
  X2
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
GeneOntology              19.34   1.97   21.36
TissueOpennessSpecificity 19.77   0.03   19.83
GenBackground              6.65   1.38   16.62
Pipelines                  1.89   0.24   17.25
MotifsInRegions            1.48   0.04   18.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
TissueOpennessSpecificity 21.31   0.03   21.41
GeneOntology              18.97   0.92   19.92
GenBackground              5.68   1.03   13.33
Pipelines                  1.83   0.14   17.41
MotifsInRegions            1.51   0.05   18.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.Rcheck/00check.log'
for details.



Installation output

enrichTF.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/enrichTF_1.8.0.tar.gz && rm -rf enrichTF.buildbin-libdir && mkdir enrichTF.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=enrichTF.buildbin-libdir enrichTF_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL enrichTF_1.8.0.zip && rm enrichTF_1.8.0.tar.gz enrichTF_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1005k  100 1005k    0     0  1846k      0 --:--:-- --:--:-- --:--:-- 1847k

install for i386

* installing *source* package 'enrichTF' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'enrichTF'
    finding HTML links ... done
    EnrichStep-class                        html  
    GenBackground                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/genBackground.html
    finding level-2 HTML links ... done

    GeneOntology                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/geneOntology.html
    MotifsInRegions                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/motifsInRegions.html
    Pipelines                               html  
    RegionConnectTargetGene                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/regionConnectTargetGene.html
    SingleSampleReport                      html  
    TFsEnrichInRegions                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tfsEnrichInRegions.html
    TissueOpennessConserve                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tissueOpennessConserve.html
    TissueOpennessSpecificity               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tissueOpennessSpecificity.html
    UnzipAndMergeBed                        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/unzipAndMergeBed.html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package can be loaded from final location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'enrichTF' ...
** testing if installed package can be loaded
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
* MD5 sums
packaged installation of 'enrichTF' as enrichTF_1.8.0.zip
* DONE (enrichTF)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'enrichTF' successfully unpacked and MD5 sums checked

Tests output

enrichTF.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Warning message:
In options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
> 
> test_check("enrichTF")
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:18 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:20 EDT"
[1] "2021-09-16 22:57:37 EDT"
[1] "2021-09-16 22:57:37 EDT"
[1] "2021-09-16 22:57:37 EDT"
[1] "2021-09-16 22:57:37 EDT"
[1] "2021-09-16 22:57:37 EDT"
[1] "2021-09-16 22:57:37 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  19.96    3.09   61.70 

enrichTF.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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

Warning message:
In options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
> 
> test_check("enrichTF")
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:07 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:08 EDT"
[1] "2021-09-16 22:58:27 EDT"
[1] "2021-09-16 22:58:27 EDT"
[1] "2021-09-16 22:58:27 EDT"
[1] "2021-09-16 22:58:27 EDT"
[1] "2021-09-16 22:58:27 EDT"
[1] "2021-09-16 22:58:27 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  23.14    1.89   48.81 

Example timings

enrichTF.Rcheck/examples_i386/enrichTF-Ex.timings

nameusersystemelapsed
GenBackground 6.65 1.3816.62
GeneOntology19.34 1.9721.36
MotifsInRegions 1.48 0.0418.99
Pipelines 1.89 0.2417.25
RegionConnectTargetGene0.830.010.84
TFsEnrichInRegions0.730.170.90
TissueOpennessConserve0.280.020.33
TissueOpennessSpecificity19.77 0.0319.83
UnzipAndMergeBed0.110.020.80

enrichTF.Rcheck/examples_x64/enrichTF-Ex.timings

nameusersystemelapsed
GenBackground 5.68 1.0313.33
GeneOntology18.97 0.9219.92
MotifsInRegions 1.51 0.0518.87
Pipelines 1.83 0.1417.41
RegionConnectTargetGene0.780.030.81
TFsEnrichInRegions0.560.090.66
TissueOpennessConserve0.190.040.23
TissueOpennessSpecificity21.31 0.0321.41
UnzipAndMergeBed0.140.040.75