Chloe H. Lee
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/proBatch |
| git_branch: master |
| git_last_commit: f9dca1a |
| git_last_commit_date: 2021-10-26 12:50:21 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:20 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the proBatch package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proBatch.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1466/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| proBatch 1.11.0 (landing page) Chloe H. Lee
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: proBatch |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:proBatch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings proBatch_1.11.0.tar.gz |
| StartedAt: 2022-03-17 19:55:26 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:59:56 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 269.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proBatch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:proBatch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings proBatch_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'proBatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proBatch' version '1.11.0'
* 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 'proBatch' 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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
calculate_PVCA 17.67 0.17 17.85
plot_PVCA.df 15.36 0.03 15.39
plot_PVCA 14.85 0.05 14.89
prepare_PVCA_df 14.47 0.01 14.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'spelling.R'
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
proBatch.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL proBatch
###
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##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'proBatch' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'proBatch'
finding HTML links ... done
calculate_PVCA html
calculate_feature_CV html
calculate_peptide_corr_distr html
calculate_sample_corr_distr html
check_sample_consistency html
color_list_to_df html
correct_batch_effects html
create_peptide_annotation html
date_to_sample_order html
dates_to_posix html
define_sample_order html
example_peptide_annotation html
example_proteome html
example_proteome_matrix html
example_sample_annotation html
feature_level_diagnostics html
fit_nonlinear html
generate_colors_for_numeric html
long_to_matrix html
matrix_to_long html
merge_rare_levels html
normalize html
plot_CV_distr html
plot_CV_distr.df html
plot_PCA html
plot_PVCA html
plot_PVCA.df html
plot_corr_matrix html
plot_heatmap_diagnostic html
plot_heatmap_generic html
plot_hierarchical_clustering html
plot_peptide_corr_distribution html
plot_protein_corrplot html
plot_sample_corr_distribution html
plot_sample_corr_heatmap html
plot_sample_mean_or_boxplot html
plot_split_violin_with_boxplot html
prepare_PVCA_df html
proBatch html
sample_annotation_to_colors html
transform_raw_data 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
* DONE (proBatch)
Making 'packages.html' ... done
proBatch.Rcheck/tests/spelling.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.20 0.01 0.20
proBatch.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(proBatch)
>
> test_check("proBatch")
[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
>
> proc.time()
user system elapsed
25.89 1.15 27.01
proBatch.Rcheck/proBatch-Ex.timings
| name | user | system | elapsed | |
| calculate_PVCA | 17.67 | 0.17 | 17.85 | |
| calculate_feature_CV | 0.33 | 0.03 | 0.36 | |
| calculate_peptide_corr_distr | 0.01 | 0.00 | 0.02 | |
| calculate_sample_corr_distr | 0.91 | 0.00 | 0.90 | |
| check_sample_consistency | 0.02 | 0.00 | 0.02 | |
| correct_batch_effects | 4.12 | 0.11 | 4.23 | |
| create_peptide_annotation | 0 | 0 | 0 | |
| date_to_sample_order | 0.09 | 0.00 | 0.10 | |
| dates_to_posix | 0.02 | 0.00 | 0.01 | |
| define_sample_order | 0.03 | 0.02 | 0.05 | |
| feature_level_diagnostics | 4.66 | 0.03 | 4.69 | |
| fit_nonlinear | 0 | 0 | 0 | |
| long_to_matrix | 0.01 | 0.03 | 0.04 | |
| matrix_to_long | 0 | 0 | 0 | |
| normalize | 0.07 | 0.00 | 0.07 | |
| plot_CV_distr | 0.53 | 0.03 | 0.56 | |
| plot_PCA | 1.15 | 0.06 | 1.22 | |
| plot_PVCA | 14.85 | 0.05 | 14.89 | |
| plot_PVCA.df | 15.36 | 0.03 | 15.39 | |
| plot_corr_matrix | 0.07 | 0.00 | 0.08 | |
| plot_heatmap_diagnostic | 2.38 | 0.10 | 2.47 | |
| plot_heatmap_generic | 0.58 | 0.01 | 0.59 | |
| plot_hierarchical_clustering | 0.42 | 0.02 | 0.44 | |
| plot_peptide_corr_distribution | 1.03 | 0.06 | 1.09 | |
| plot_protein_corrplot | 0.24 | 0.00 | 0.24 | |
| plot_sample_corr_distribution | 1.37 | 0.02 | 1.39 | |
| plot_sample_corr_heatmap | 0.59 | 0.01 | 0.61 | |
| plot_sample_mean_or_boxplot | 2.80 | 0.02 | 2.81 | |
| prepare_PVCA_df | 14.47 | 0.01 | 14.48 | |
| sample_annotation_to_colors | 0.06 | 0.00 | 0.06 | |
| transform_raw_data | 0 | 0 | 0 | |