Chloe H. Lee
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/proBatch |
| git_branch: RELEASE_3_13 |
| git_last_commit: a577fe3 |
| git_last_commit_date: 2021-05-19 12:42:05 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
|
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 1434/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| proBatch 1.8.0 (landing page) Chloe H. Lee
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: proBatch |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings proBatch_1.8.0.tar.gz |
| StartedAt: 2021-10-14 11:06:04 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:10:47 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 283.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proBatch.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings proBatch_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/proBatch.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.8.0’
* 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 ‘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 16.447 0.404 16.852
plot_PVCA.df 16.066 0.012 16.078
plot_PVCA 16.024 0.000 16.025
prepare_PVCA_df 15.963 0.004 15.970
correct_batch_effects 6.437 0.100 6.531
feature_level_diagnostics 6.121 0.004 6.126
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL proBatch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 ** 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)
proBatch.Rcheck/tests/spelling.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
0.161 0.026 0.177
proBatch.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 ]
>
> proc.time()
user system elapsed
30.572 0.882 31.460
proBatch.Rcheck/proBatch-Ex.timings
| name | user | system | elapsed | |
| calculate_PVCA | 16.447 | 0.404 | 16.852 | |
| calculate_feature_CV | 0.998 | 0.280 | 1.278 | |
| calculate_peptide_corr_distr | 0.026 | 0.000 | 0.026 | |
| calculate_sample_corr_distr | 1.240 | 0.008 | 1.248 | |
| check_sample_consistency | 0.012 | 0.004 | 0.016 | |
| correct_batch_effects | 6.437 | 0.100 | 6.531 | |
| create_peptide_annotation | 0.005 | 0.000 | 0.005 | |
| date_to_sample_order | 0.113 | 0.004 | 0.117 | |
| dates_to_posix | 0.009 | 0.000 | 0.009 | |
| define_sample_order | 0.014 | 0.000 | 0.014 | |
| feature_level_diagnostics | 6.121 | 0.004 | 6.126 | |
| fit_nonlinear | 0.008 | 0.000 | 0.009 | |
| long_to_matrix | 0.045 | 0.000 | 0.046 | |
| matrix_to_long | 0.01 | 0.00 | 0.01 | |
| normalize | 0.1 | 0.0 | 0.1 | |
| plot_CV_distr | 0.576 | 0.024 | 0.599 | |
| plot_PCA | 1.33 | 0.00 | 1.33 | |
| plot_PVCA | 16.024 | 0.000 | 16.025 | |
| plot_PVCA.df | 16.066 | 0.012 | 16.078 | |
| plot_corr_matrix | 0.035 | 0.000 | 0.034 | |
| plot_heatmap_diagnostic | 1.220 | 0.024 | 1.244 | |
| plot_heatmap_generic | 0.563 | 0.016 | 0.581 | |
| plot_hierarchical_clustering | 0.366 | 0.004 | 0.370 | |
| plot_peptide_corr_distribution | 1.224 | 0.000 | 1.223 | |
| plot_protein_corrplot | 0.171 | 0.004 | 0.175 | |
| plot_sample_corr_distribution | 1.268 | 0.000 | 1.268 | |
| plot_sample_corr_heatmap | 0.477 | 0.000 | 0.477 | |
| plot_sample_mean_or_boxplot | 3.364 | 0.008 | 3.373 | |
| prepare_PVCA_df | 15.963 | 0.004 | 15.970 | |
| sample_annotation_to_colors | 0.03 | 0.00 | 0.03 | |
| transform_raw_data | 0.008 | 0.000 | 0.008 | |