Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1846/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scBubbletree 1.9.0  (landing page)
Simo Kitanovski
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/scBubbletree
git_branch: devel
git_last_commit: 2950075
git_last_commit_date: 2024-10-29 11:14:42 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: scBubbletree
Version: 1.9.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scBubbletree_1.9.0.tar.gz
StartedAt: 2024-12-24 10:51:04 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 11:03:02 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 718.6 seconds
RetCode: 0
Status:   OK  
CheckDir: scBubbletree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scBubbletree_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBubbletree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scBubbletree’ version ‘1.9.0’
* 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 ‘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 loading without being on the library search path ... 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 41.776  0.519  42.400
get_num_cell_tiles        26.761  0.012  26.826
get_num_tiles             26.667  0.004  26.723
get_bubbletree_kmeans     26.316  0.024  26.414
get_bubbletree_graph      23.522  0.036  23.619
get_num_violins           22.629  0.012  22.678
get_cat_tiles             21.290  0.011  21.355
get_r                     18.469  0.036  19.368
get_bubbletree_dummy      16.578  0.072  16.684
get_gini_k                13.510  0.020  13.558
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck/00check.log’
for details.


Installation output

scBubbletree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scBubbletree
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
323.919   1.455 326.374 

Example timings

scBubbletree.Rcheck/scBubbletree-Ex.timings

nameusersystemelapsed
d_5000.0070.0000.007
d_ccl0.0180.0000.018
get_bubbletree_comparison41.776 0.51942.400
get_bubbletree_dummy16.578 0.07216.684
get_bubbletree_graph23.522 0.03623.619
get_bubbletree_kmeans26.316 0.02426.414
get_cat_tiles21.290 0.01121.355
get_gini0.0020.0000.003
get_gini_k13.510 0.02013.558
get_k4.0260.0084.042
get_num_cell_tiles26.761 0.01226.826
get_num_tiles26.667 0.00426.723
get_num_violins22.629 0.01222.678
get_r18.469 0.03619.368