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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 244/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.30.0  (landing page)
Todd Creasy , Wei Zhu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/BubbleTree
git_branch: RELEASE_3_17
git_last_commit: 8686dde
git_last_commit_date: 2023-04-25 10:37:41 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BubbleTree on kjohnson2


To the developers/maintainers of the BubbleTree package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BubbleTree
Version: 2.30.0
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_2.30.0.tar.gz
StartedAt: 2023-10-17 06:54:02 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 07:03:47 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 584.6 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_2.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BubbleTree.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BubbleTree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BubbleTree’ version ‘2.30.0’
* 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 23.8Mb
  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         18.624  0.348  28.225
heteroLociTrack  6.490  0.190   9.264
* 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-3.17-bioc-mac-arm64/meat/BubbleTree.Rcheck/00check.log’
for details.



Installation output

BubbleTree.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
Annotate0.0000.0000.001
BTreePlotter1.0700.0181.608
BTreePredictor0.0070.0000.011
RBD0.0010.0000.001
RscoreTrack0.6040.0260.945
TrackPlotter000
annoByGenesAndCyto0.6350.0530.982
bafTrack0.3540.0270.540
btcompare0.0030.0030.008
btpredict2.9110.1164.411
drawBTree0.3370.0200.523
drawBubbles0.3550.0110.551
drawFeatures1.3520.0422.128
getTracks0.7150.0221.083
heteroLociTrack6.4900.1909.264
info2.8530.0503.705
loadRBD0.0230.0010.034
makeRBD18.624 0.34828.225
saveXLS0.3850.1140.873
trackBTree0.3490.0130.539
xyTrack0.2920.0190.463