| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:24 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the CyTOFpower package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CyTOFpower.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 438/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CyTOFpower 1.0.0 (landing page) Anne-Maud Ferreira
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CyTOFpower |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CyTOFpower.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CyTOFpower_1.0.0.tar.gz |
| StartedAt: 2022-04-12 18:08:06 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 18:10:08 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 122.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CyTOFpower.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CyTOFpower.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CyTOFpower_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CyTOFpower.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CyTOFpower/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CyTOFpower' version '1.0.0' * 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 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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * 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: OK
CyTOFpower.Rcheck/00install.out
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##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CyTOFpower_1.0.0.tar.gz && rm -rf CyTOFpower.buildbin-libdir && mkdir CyTOFpower.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CyTOFpower.buildbin-libdir CyTOFpower_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CyTOFpower_1.0.0.zip && rm CyTOFpower_1.0.0.tar.gz CyTOFpower_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 95249 100 95249 0 0 488k 0 --:--:-- --:--:-- --:--:-- 489k
install for i386
* installing *source* package 'CyTOFpower' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CyTOFpower'
finding HTML links ... done
CyTOFpower html
compute_effectsize html
compute_pwr html
compute_variance html
function_DEmarkers_sup_nbmarkers html
function_apply_modelcomputations_modelchoice
html
function_apply_onesimulation_withmarkerinfo
html
function_check_nbDEmarkers html
function_check_nbmarkers html
function_compute_diffcyt_features html
function_create_mock_dataset_withmarkerinfo
html
function_desigmat_contrast_diffcytDSlimma_fixedeffect
html
function_desigmat_contrast_diffcytDSlimma_randomeffect
html
function_extract_marker_names html
function_formula_contrast_diffcytDSLMM_randomeffect
html
function_is_data_paired html
function_names_DE_markers html
function_run_bootstrapcytoGLMM html
function_run_cytoGLMM html
function_run_diffcytDSLMM html
function_run_diffcytDSlimma html
function_run_diffcyt_full_pipeline html
function_summary_results_models html
function_to_compute_model_computation_onesimulation_modelchoice
html
function_to_transform_data html
function_value_onemarker html
** 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
install for x64
* installing *source* package 'CyTOFpower' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CyTOFpower' as CyTOFpower_1.0.0.zip
* DONE (CyTOFpower)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CyTOFpower' successfully unpacked and MD5 sums checked
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CyTOFpower.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, by = "markers"
Joining, 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 11 | SKIP 0 | PASS 69 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 69 ]
>
> proc.time()
user system elapsed
17.60 2.10 26.96
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CyTOFpower.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, by = "markers"
Joining, 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 11 | SKIP 0 | PASS 69 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 69 ]
>
> proc.time()
user system elapsed
20.18 0.92 21.09
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CyTOFpower.Rcheck/examples_i386/CyTOFpower-Ex.timings
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CyTOFpower.Rcheck/examples_x64/CyTOFpower-Ex.timings
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