Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:47 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proBatch_1.8.0.tar.gz |
StartedAt: 2021-10-14 22:32:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:38:43 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 386.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: proBatch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proBatch_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/proBatch.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed prepare_PVCA_df 24.236 0.052 24.311 calculate_PVCA 23.815 0.094 23.928 plot_PVCA 22.855 0.068 22.936 plot_PVCA.df 22.817 0.043 22.876 correct_batch_effects 8.169 0.180 8.354 feature_level_diagnostics 5.084 0.066 5.158 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/proBatch.Rcheck/00check.log’ for details.
proBatch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proBatch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 0.311 0.069 0.357
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-apple-darwin17.0 (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 43.741 0.921 44.688
proBatch.Rcheck/proBatch-Ex.timings
name | user | system | elapsed | |
calculate_PVCA | 23.815 | 0.094 | 23.928 | |
calculate_feature_CV | 1.000 | 0.017 | 1.019 | |
calculate_peptide_corr_distr | 0.035 | 0.000 | 0.036 | |
calculate_sample_corr_distr | 0.840 | 0.020 | 0.861 | |
check_sample_consistency | 0.047 | 0.006 | 0.053 | |
correct_batch_effects | 8.169 | 0.180 | 8.354 | |
create_peptide_annotation | 0.008 | 0.001 | 0.008 | |
date_to_sample_order | 0.284 | 0.001 | 0.285 | |
dates_to_posix | 0.014 | 0.000 | 0.015 | |
define_sample_order | 0.014 | 0.002 | 0.014 | |
feature_level_diagnostics | 5.084 | 0.066 | 5.158 | |
fit_nonlinear | 0.010 | 0.000 | 0.011 | |
long_to_matrix | 0.050 | 0.000 | 0.049 | |
matrix_to_long | 0.014 | 0.000 | 0.014 | |
normalize | 0.109 | 0.002 | 0.111 | |
plot_CV_distr | 0.923 | 0.018 | 0.942 | |
plot_PCA | 1.347 | 0.042 | 1.390 | |
plot_PVCA | 22.855 | 0.068 | 22.936 | |
plot_PVCA.df | 22.817 | 0.043 | 22.876 | |
plot_corr_matrix | 0.038 | 0.002 | 0.039 | |
plot_heatmap_diagnostic | 1.838 | 0.087 | 1.938 | |
plot_heatmap_generic | 0.768 | 0.048 | 0.819 | |
plot_hierarchical_clustering | 0.567 | 0.021 | 0.591 | |
plot_peptide_corr_distribution | 1.438 | 0.035 | 1.473 | |
plot_protein_corrplot | 0.272 | 0.005 | 0.277 | |
plot_sample_corr_distribution | 1.293 | 0.018 | 1.312 | |
plot_sample_corr_heatmap | 0.662 | 0.029 | 0.691 | |
plot_sample_mean_or_boxplot | 4.016 | 0.053 | 4.076 | |
prepare_PVCA_df | 24.236 | 0.052 | 24.311 | |
sample_annotation_to_colors | 0.051 | 0.001 | 0.052 | |
transform_raw_data | 0.009 | 0.001 | 0.010 | |