Jelena Cuklina
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/proBatch |
| Branch: master |
| Last Commit: 6241f81 |
| Last Changed Date: 2019-10-29 13:43:31 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:53:43 -0500 (Thu, 16 Jan 2020).
| Package 1301/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proBatch 1.3.0 Jelena Cuklina
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: proBatch |
| Version: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2020-01-16 07:39:53 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:47:26 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 452.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proBatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/proBatch.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.3.0’
* 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 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
calculate_PVCA 24.492 0.177 24.676
plot_PVCA 23.953 0.123 24.083
prepare_PVCA_df 23.642 0.082 23.731
plot_PVCA.df 23.358 0.090 23.454
correct_batch_effects 15.524 2.664 18.194
plot_sample_mean_or_boxplot 6.520 0.207 6.740
feature_level_diagnostics 5.750 0.093 5.845
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proBatch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
0.413 0.156 0.518
proBatch.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
Standardizing Data across genes
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 159 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ]
>
> proc.time()
user system elapsed
48.096 2.045 50.105
proBatch.Rcheck/proBatch-Ex.timings
| name | user | system | elapsed | |
| calculate_PVCA | 24.492 | 0.177 | 24.676 | |
| calculate_feature_CV | 0.715 | 0.065 | 0.779 | |
| calculate_peptide_corr_distr | 0.034 | 0.001 | 0.034 | |
| calculate_sample_corr_distr | 1.627 | 0.089 | 1.716 | |
| check_sample_consistency | 0.040 | 0.016 | 0.056 | |
| correct_batch_effects | 15.524 | 2.664 | 18.194 | |
| create_peptide_annotation | 0.013 | 0.001 | 0.013 | |
| date_to_sample_order | 0.359 | 0.010 | 0.368 | |
| dates_to_posix | 0.013 | 0.002 | 0.015 | |
| define_sample_order | 0.033 | 0.014 | 0.048 | |
| feature_level_diagnostics | 5.750 | 0.093 | 5.845 | |
| fit_nonlinear | 0.019 | 0.000 | 0.020 | |
| long_to_matrix | 0.080 | 0.018 | 0.099 | |
| matrix_to_long | 0.025 | 0.003 | 0.027 | |
| normalize | 0.109 | 0.013 | 0.122 | |
| plot_CV_distr | 2.164 | 0.245 | 2.410 | |
| plot_PCA | 1.044 | 0.141 | 1.185 | |
| plot_PVCA | 23.953 | 0.123 | 24.083 | |
| plot_PVCA.df | 23.358 | 0.090 | 23.454 | |
| plot_corr_matrix | 0.068 | 0.003 | 0.071 | |
| plot_heatmap_diagnostic | 2.684 | 0.243 | 2.948 | |
| plot_heatmap_generic | 1.269 | 0.087 | 1.387 | |
| plot_hierarchical_clustering | 0.612 | 0.081 | 0.699 | |
| plot_peptide_corr_distribution | 1.864 | 0.174 | 2.038 | |
| plot_protein_corrplot | 0.322 | 0.005 | 0.328 | |
| plot_sample_corr_distribution | 1.929 | 0.195 | 2.125 | |
| plot_sample_corr_heatmap | 1.075 | 0.067 | 1.144 | |
| plot_sample_mean_or_boxplot | 6.520 | 0.207 | 6.740 | |
| prepare_PVCA_df | 23.642 | 0.082 | 23.731 | |
| sample_annotation_to_colors | 0.037 | 0.000 | 0.039 | |
| transform_raw_data | 0.009 | 0.003 | 0.013 | |