Multiple platform build/check report for BioC 3.21 - CHECK results for CyTOFpower on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4749
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4461
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4411
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4366
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4241
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 CyTOFpower on kunpeng2

To the developers/maintainers of the CyTOFpower package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/CyTOFpower.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: CyTOFpower

Version: 1.13.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CyTOFpower_1.13.0.tar.gz

StartedAt: 2024-12-09 05:00:22 -0000 (Mon, 09 Dec 2024)

EndedAt: 2024-12-09 05:01:38 -0000 (Mon, 09 Dec 2024)

EllapsedTime: 76.1 seconds

RetCode: 0

Status: OK

CheckDir: CyTOFpower.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CyTOFpower_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CyTOFpower.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CyTOFpower/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CyTOFpower’ version ‘1.13.0’
* 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 ‘CyTOFpower’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Changes in version 0.99.0 (2021-09-15)
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CyTOFpower.Rcheck/00check.log’
for details.

Installation output

CyTOFpower.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘CyTOFpower’ ...
** using staged installation
** R
** 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 (CyTOFpower)

Tests output

CyTOFpower.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(CyTOFpower)
> 
> test_check("CyTOFpower")
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  1

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  1

  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

Joining with `by = join_by(markers)`
Joining with `by = join_by(markers)`
boundary (singular) fit: see help('isSingular')
Fitting linear models with random effects term for 'block_id'.
boundary (singular) fit: see help('isSingular')
Run the limma model with random effect
Fitting linear models with random effects term for 'block_id'.
Run the limma model with fixed effect
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the limma model with random effect
Fitting linear models with random effects term for 'block_id'.
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the limma model with fixed effect
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 69 ]

[ FAIL 0 | WARN 32 | SKIP 0 | PASS 69 ]
> 
> proc.time()
   user  system elapsed 
 23.936   1.162  25.053

Example timings

CyTOFpower.Rcheck/CyTOFpower-Ex.timings

name	user	system	elapsed
CyTOFpower	0	0	0