Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-24 11:05:51 -0400 (Fri, 24 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4286
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4276
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4303
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 palomino4


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? 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 231/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.28.0  (landing page)
Todd Creasy , Wei Zhu
Snapshot Date: 2023-03-22 14:00:04 -0400 (Wed, 22 Mar 2023)
git_url: https://git.bioconductor.org/packages/BubbleTree
git_branch: RELEASE_3_16
git_last_commit: a9640da
git_last_commit_date: 2022-11-01 11:11:07 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BubbleTree
Version: 2.28.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BubbleTree.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BubbleTree_2.28.0.tar.gz
StartedAt: 2023-03-22 23:39:49 -0400 (Wed, 22 Mar 2023)
EndedAt: 2023-03-22 23:45:34 -0400 (Wed, 22 Mar 2023)
EllapsedTime: 345.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BubbleTree.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BubbleTree_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BubbleTree.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.28.0'
* 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 whether package 'BubbleTree' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.8Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  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         14.31   0.20   14.52
heteroLociTrack  5.08   0.11    5.18
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.



Installation output

BubbleTree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BubbleTree
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'BubbleTree' ...
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  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
Annotate000
BTreePlotter0.220.010.24
BTreePredictor000
RBD000
RscoreTrack0.520.020.53
TrackPlotter000
annoByGenesAndCyto0.420.080.50
bafTrack0.250.010.26
btcompare000
btpredict2.570.142.72
drawBTree0.280.020.30
drawBubbles0.270.010.28
drawFeatures1.140.021.16
getTracks1.640.051.69
heteroLociTrack5.080.115.18
info3.160.093.25
loadRBD0.030.000.03
makeRBD14.31 0.2014.52
saveXLS0.140.001.55
trackBTree0.250.000.25
xyTrack0.230.000.23