| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 479/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CyTOFpower 1.6.0 (landing page) Anne-Maud Ferreira
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the CyTOFpower 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. |
| Package: CyTOFpower |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CyTOFpower_1.6.0.tar.gz |
| StartedAt: 2023-10-17 13:37:26 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 13:39:19 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 113.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CyTOFpower.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CyTOFpower_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CyTOFpower.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 ‘CyTOFpower/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CyTOFpower’ version ‘1.6.0’
* 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 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 ... 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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 1 | WARN 26 | SKIP 0 | PASS 68 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_run_models.R:85:3'): Run the CytoGLMM - GLMM model ───────────
`cytoglmm_res <- function_run_cytoGLMM(mock_dataset = ls_3markers$ls_mock_data)` did not throw the expected warning.
[ FAIL 1 | WARN 26 | SKIP 0 | PASS 68 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CyTOFpower.Rcheck/00check.log’
for details.
CyTOFpower.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CyTOFpower ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)
CyTOFpower.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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 1 | WARN 26 | SKIP 0 | PASS 68 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_run_models.R:85:3'): Run the CytoGLMM - GLMM model ───────────
`cytoglmm_res <- function_run_cytoGLMM(mock_dataset = ls_3markers$ls_mock_data)` did not throw the expected warning.
[ FAIL 1 | WARN 26 | SKIP 0 | PASS 68 ]
Error: Test failures
Execution halted
CyTOFpower.Rcheck/CyTOFpower-Ex.timings
| name | user | system | elapsed | |
| CyTOFpower | 0.000 | 0.001 | 0.001 | |