Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:46 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 segmenter on machv2


To the developers/maintainers of the segmenter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmenter.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 1754/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmenter 1.0.0  (landing page)
Mahmoud Ahmed
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/segmenter
git_branch: RELEASE_3_14
git_last_commit: 45aa76e
git_last_commit_date: 2021-10-26 13:10:57 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: segmenter
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmenter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmenter_1.0.0.tar.gz
StartedAt: 2022-04-12 18:22:42 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:34:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 709.3 seconds
RetCode: 0
Status:   OK  
CheckDir: segmenter.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmenter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmenter_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/segmenter.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmenter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmenter’ version ‘1.0.0’
* 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 ‘segmenter’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
learn_model       39.450  2.074  22.341
binarize_bam      30.354  6.958  17.684
annotate_segments 34.215  1.485  36.463
read_bins_file     4.322  0.981   5.352
* 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

segmenter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘segmenter’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (segmenter)

Tests output

segmenter.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(segmenter)

> 
> test_check("segmenter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
310.297  15.448 216.344 

Example timings

segmenter.Rcheck/segmenter-Ex.timings

nameusersystemelapsed
accessors0.1430.0110.154
annotate_segments34.215 1.48536.463
binarize_bam30.354 6.95817.684
compare_models0.0040.0010.006
emissions_file0.0000.0000.001
enrichment_files0.0010.0010.001
get_frequency0.0290.0010.029
get_width0.6231.0791.823
learn_model39.450 2.07422.341
methods0.0010.0010.002
model_file0.0000.0010.001
overlap_files0.0000.0010.001
plot_heatmap0.7510.0190.773
read_bam_file0.0450.0030.047
read_bins_file4.3220.9815.352
read_cellmark_file0.0030.0010.003
read_chromsize_file0.0030.0020.004
read_emissions_file0.0020.0010.004
read_enrichment_file0.0040.0010.005
read_model_file0.0060.0040.009
read_overlap_file0.0020.0010.003
read_segements_file0.0520.0030.055
read_transitions_file0.0020.0010.003
segments_files0.0000.0010.001
tidy_ranges0.0820.0020.083
transitions_file0.0010.0000.000