Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-29 11:04:44 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4301
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 consensusSeekeR on nebbiolo1


To the developers/maintainers of the consensusSeekeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consensusSeekeR.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 414/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.27.0  (landing page)
Astrid Deschenes
Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023)
git_url: https://git.bioconductor.org/packages/consensusSeekeR
git_branch: devel
git_last_commit: 33153bc
git_last_commit_date: 2022-11-01 11:12:31 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: consensusSeekeR
Version: 1.27.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings consensusSeekeR_1.27.0.tar.gz
StartedAt: 2023-03-28 19:12:58 -0400 (Tue, 28 Mar 2023)
EndedAt: 2023-03-28 19:17:51 -0400 (Tue, 28 Mar 2023)
EllapsedTime: 293.4 seconds
RetCode: 0
Status:   OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings consensusSeekeR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/consensusSeekeR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.27.0’
* 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 ‘consensusSeekeR’ 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘consensusSeekeR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

consensusSeekeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL consensusSeekeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘consensusSeekeR’ ...
** using staged installation
** R
** data
** 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 (consensusSeekeR)

Tests output

consensusSeekeR.Rcheck/tests/runTests.Rout


R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 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.

> ## Run all tests present in the package
> BiocGenerics:::testPackage("consensusSeekeR")

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, aperm, 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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname



RUNIT TEST PROTOCOL -- Tue Mar 28 19:16:39 2023 
*********************************************** 
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensusSeekeR RUnit Tests - 56 test functions, 0 errors, 0 failures
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 14.162   0.708  14.862 

Example timings

consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.6570.1370.794
A549_CTCF_MYJ_Peaks_partial0.3260.0160.343
A549_CTCF_MYN_NarrowPeaks_partial0.2810.0090.289
A549_CTCF_MYN_Peaks_partial0.3820.0000.383
A549_FOSL2_01_NarrowPeaks_partial0.2760.0030.280
A549_FOSL2_01_Peaks_partial0.3320.0080.340
A549_FOXA1_01_NarrowPeaks_partial0.3620.0000.362
A549_FOXA1_01_Peaks_partial0.5130.0190.532
A549_NR3C1_CFQ_NarrowPeaks_partial0.3080.0280.336
A549_NR3C1_CFQ_Peaks_partial0.3730.0120.384
A549_NR3C1_CFR_NarrowPeaks_partial0.2940.0080.302
A549_NR3C1_CFR_Peaks_partial0.2860.0090.294
A549_NR3C1_CFS_NarrowPeaks_partial0.7570.0110.769
A549_NR3C1_CFS_Peaks_partial0.6920.0040.696
NOrMAL_nucleosome_positions0.5560.0170.573
NOrMAL_nucleosome_ranges0.5530.0040.558
NucPosSimulator_nucleosome_positions0.5380.0040.542
NucPosSimulator_nucleosome_ranges0.5660.0000.566
PING_nucleosome_positions0.3650.0200.384
PING_nucleosome_ranges0.3300.0040.334
findConsensusPeakRegions0.6910.0190.711
findConsensusPeakRegionsValidation0.0720.0080.080
readNarrowPeakFile0.0820.0030.086