Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:04 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 regutools on palomino4


To the developers/maintainers of the regutools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regutools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1601/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regutools 1.9.0  (landing page)
Joselyn Chavez
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/regutools
git_branch: master
git_last_commit: 01322b5
git_last_commit_date: 2022-04-26 12:05:06 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: regutools
Version: 1.9.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regutools.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings regutools_1.9.0.tar.gz
StartedAt: 2022-06-24 04:57:56 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:06:38 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 521.1 seconds
RetCode: 0
Status:   OK  
CheckDir: regutools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regutools.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings regutools_1.9.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/regutools.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'regutools/DESCRIPTION' ... OK
* this is package 'regutools' version '1.9.0'
* 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 'regutools' 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_dna_objects       10.50   0.59   11.22
build_condition         7.86   0.38    8.50
get_gene_regulators     6.65   0.29    7.18
convert_to_biostrings   6.38   0.37    7.25
guess_id                5.86   0.40    6.34
convert_to_granges      5.89   0.36    6.35
get_dna_objects         5.89   0.35    6.49
get_dataset             5.69   0.45    6.25
connect_database        5.78   0.34    6.22
regulondb               5.69   0.33    6.12
get_regulatory_summary  5.57   0.38    6.05
list_datasets           5.38   0.41    5.89
get_gene_synonyms       5.46   0.32    5.89
get_binding_sites       5.39   0.36    5.86
get_regulatory_network  5.46   0.29    8.24
list_attributes         5.29   0.28    5.69
* 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: OK


Installation output

regutools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/regutools_1.9.0.tar.gz && rm -rf regutools.buildbin-libdir && mkdir regutools.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regutools.buildbin-libdir regutools_1.9.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL regutools_1.9.0.zip && rm regutools_1.9.0.tar.gz regutools_1.9.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  494k  100  494k    0     0  4627k      0 --:--:-- --:--:-- --:--:-- 4661k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'regutools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'regutools' as regutools_1.9.0.zip
* DONE (regutools)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'regutools' successfully unpacked and MD5 sums checked

Tests output

regutools.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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("regutools")
> 
> test_check("regutools")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 110 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 106.78    6.67  117.45 

Example timings

regutools.Rcheck/regutools-Ex.timings

nameusersystemelapsed
build_condition7.860.388.50
connect_database5.780.346.22
convert_to_biostrings6.380.377.25
convert_to_granges5.890.366.35
existing_intervals000
existing_partial_match000
get_binding_sites5.390.365.86
get_dataset5.690.456.25
get_dna_objects5.890.356.49
get_gene_regulators6.650.297.18
get_gene_synonyms5.460.325.89
get_regulatory_network5.460.298.24
get_regulatory_summary5.570.386.05
guess_id5.860.406.34
list_attributes5.290.285.69
list_datasets5.380.415.89
non_existing_intervals000
plot_dna_objects10.50 0.5911.22
regulondb5.690.336.12