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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1861/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scBubbletree 1.8.0  (landing page)
Simo Kitanovski
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/scBubbletree
git_branch: RELEASE_3_20
git_last_commit: a0f6882
git_last_commit_date: 2024-10-29 11:14:42 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for scBubbletree on lconway

To the developers/maintainers of the scBubbletree package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scBubbletree.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: scBubbletree
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.8.0.tar.gz
StartedAt: 2024-11-20 02:18:19 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 02:29:22 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 663.6 seconds
RetCode: 0
Status:   OK  
CheckDir: scBubbletree.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBubbletree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scBubbletree’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘scBubbletree’ 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 code 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 ... NOTE
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compare_bubbletrees: no visible binding for global variable ‘isTip’
compare_bubbletrees: no visible binding for global variable ‘Cells’
compare_bubbletrees: no visible binding for global variable ‘lab_short’
compare_bubbletrees: no visible binding for global variable ‘label’
compare_bubbletrees: no visible binding for global variable ‘JD’
compare_bubbletrees: no visible binding for global variable
  ‘intersection’
get_dendrogram: no visible binding for global variable ‘isTip’
get_dendrogram: no visible binding for global variable ‘Cells’
get_dendrogram: no visible binding for global variable ‘label’
get_dendrogram: no visible binding for global variable ‘lab_short’
get_dendrogram: no visible binding for global variable ‘lab_long’
get_num_cell_tiles: no visible binding for global variable ‘cluster’
ggplot_cat_tiles: no visible binding for global variable ‘feature’
ggplot_cat_tiles: no visible binding for global variable ‘cluster’
ggplot_cat_tiles: no visible binding for global variable ‘percent’
ggplot_num_cell_tiles: no visible binding for global variable ‘cluster’
ggplot_num_cell_tiles: no visible binding for global variable ‘f’
ggplot_num_tiles: no visible binding for global variable ‘feature’
ggplot_num_tiles: no visible binding for global variable ‘cluster’
ggplot_num_tiles: no visible binding for global variable ‘value’
ggplot_num_violins: no visible binding for global variable ‘cluster’
ggplot_num_violins: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Cells JD cluster f feature intersection isTip lab_long lab_short
  label percent value
* 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
get_bubbletree_comparison 19.427  0.295  19.811
get_r                     12.827  0.744  13.625
get_bubbletree_kmeans     11.766  0.127  11.956
get_num_tiles             11.470  0.090  11.576
get_num_cell_tiles        11.335  0.106  11.467
get_bubbletree_graph      10.091  0.181  10.324
get_num_violins            9.249  0.166   9.448
get_gini_k                 8.438  0.402   8.883
get_cat_tiles              8.406  0.100   8.539
get_bubbletree_dummy       5.950  0.070   6.047
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/scBubbletree.Rcheck/00check.log’
for details.


Installation output

scBubbletree.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘scBubbletree’ ...
** 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 (scBubbletree)

Tests output

scBubbletree.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(scBubbletree)
> 
> test_check("scBubbletree")
Tests input rules of get_bubbletree_graph 
Tests input rules of get_bubbletree_kmeans 
Tests input rules of get_cat_tiles 
Tests input rules of get_gini_k 
Tests input rules of get_gini 
Tests input rules of get_k 
Tests input rules of get_num_tiles 
Tests input rules of get_num_violins 
Tests input rules of get_r 
Tests input rules of util 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 477 ]
> 
> proc.time()
   user  system elapsed 
209.077   7.723 218.055 

Example timings

scBubbletree.Rcheck/scBubbletree-Ex.timings

nameusersystemelapsed
d_5000.0060.0020.006
d_ccl0.0140.0010.015
get_bubbletree_comparison19.427 0.29519.811
get_bubbletree_dummy5.9500.0706.047
get_bubbletree_graph10.091 0.18110.324
get_bubbletree_kmeans11.766 0.12711.956
get_cat_tiles8.4060.1008.539
get_gini0.0020.0000.002
get_gini_k8.4380.4028.883
get_k1.9410.1102.060
get_num_cell_tiles11.335 0.10611.467
get_num_tiles11.470 0.09011.576
get_num_violins9.2490.1669.448
get_r12.827 0.74413.625