Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:22 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 BubbleTree on machv2


To the developers/maintainers of the BubbleTree package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BubbleTree.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 222/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.24.0  (landing page)
Todd Creasy , Wei Zhu
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/BubbleTree
git_branch: RELEASE_3_14
git_last_commit: c74ad0d
git_last_commit_date: 2021-10-26 12:18:49 -0500 (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: BubbleTree
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BubbleTree_2.24.0.tar.gz
StartedAt: 2022-01-16 10:52:19 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 11:00:31 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 492.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BubbleTree_2.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BubbleTree.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BubbleTree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BubbleTree’ version ‘2.24.0’
* 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 ‘BubbleTree’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.9Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
 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 ... NOTE
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
Undefined global functions or variables:
  queryHits
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
makeRBD         30.716  0.082  31.226
heteroLociTrack  8.041  0.254   8.310
btpredict        5.271  0.174   5.447
info             5.240  0.051   5.321
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.



Installation output

BubbleTree.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BubbleTree’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
** 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 (BubbleTree)

Tests output


Example timings

BubbleTree.Rcheck/BubbleTree-Ex.timings

nameusersystemelapsed
Annotate0.0000.0010.001
BTreePlotter0.1340.0140.149
BTreePredictor0.0080.0010.008
RBD000
RscoreTrack0.9300.0180.949
TrackPlotter0.0000.0000.001
annoByGenesAndCyto0.8210.0280.850
bafTrack0.4850.0090.494
btcompare0.0030.0010.003
btpredict5.2710.1745.447
drawBTree0.3710.0070.378
drawBubbles0.4330.0060.439
drawFeatures1.7230.0211.746
getTracks2.1010.0322.135
heteroLociTrack8.0410.2548.310
info5.2400.0515.321
loadRBD0.0400.0030.042
makeRBD30.716 0.08231.226
saveXLS0.5580.0850.671
trackBTree0.4420.0070.450
xyTrack0.3720.0050.376