Chloe H. Lee
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/proBatch |
| Branch: RELEASE_3_9 |
| Last Commit: 6640beb |
| Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:17:45 -0400 (Wed, 16 Oct 2019).
| Package 1251/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proBatch 1.0.0 Chloe H. Lee
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.0.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings proBatch_1.0.0.tar.gz |
| StartedAt: 2019-10-16 04:04:50 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:09:24 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 274.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proBatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings proBatch_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/proBatch.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_with_fitting_curve 36.563 0.884 37.464
adjust_batch_trend 34.112 3.059 37.186
correct_batch_effects 30.875 1.092 31.977
plot_PVCA 5.227 0.012 5.272
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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-3.9-bioc/R/bin/R CMD INSTALL proBatch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
Standardizing Data across genes
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 144 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.084 0.860 20.257
proBatch.Rcheck/proBatch-Ex.timings
| name | user | system | elapsed | |
| adjust_batch_trend | 34.112 | 3.059 | 37.186 | |
| center_peptide_batch_medians | 1.275 | 0.000 | 1.274 | |
| correct_batch_effects | 30.875 | 1.092 | 31.977 | |
| correct_with_ComBat | 1.953 | 0.315 | 2.264 | |
| create_peptide_annotation | 0.017 | 0.002 | 0.021 | |
| date_to_sample_order | 0.163 | 0.004 | 0.166 | |
| dates_to_posix | 0.005 | 0.000 | 0.004 | |
| log_transform | 0.004 | 0.000 | 0.004 | |
| long_to_matrix | 0.082 | 0.003 | 0.086 | |
| matrix_to_long | 0.402 | 0.008 | 0.410 | |
| normalize_data | 0.038 | 0.001 | 0.039 | |
| normalize_sample_medians | 0.047 | 0.000 | 0.047 | |
| plot_PCA | 0.248 | 0.000 | 0.248 | |
| plot_PVCA | 5.227 | 0.012 | 5.272 | |
| plot_corr_matrix | 0.019 | 0.000 | 0.018 | |
| plot_heatmap | 1.675 | 0.012 | 1.687 | |
| plot_hierarchical_clustering | 0.329 | 0.004 | 0.333 | |
| plot_iRT | 0.101 | 0.000 | 0.101 | |
| plot_peptide_corr_distribution | 3.563 | 0.012 | 3.579 | |
| plot_peptides_of_one_protein | 0.060 | 0.004 | 0.063 | |
| plot_protein_corrplot | 0.084 | 0.000 | 0.083 | |
| plot_sample_corr_distribution | 0.660 | 0.008 | 0.667 | |
| plot_sample_corr_heatmap | 0.049 | 0.000 | 0.049 | |
| plot_sample_mean_or_boxplot | 0.674 | 0.003 | 0.678 | |
| plot_single_feature | 0.03 | 0.00 | 0.03 | |
| plot_spike_in | 0.092 | 0.000 | 0.093 | |
| plot_with_fitting_curve | 36.563 | 0.884 | 37.464 | |
| quantile_normalize | 0.043 | 0.000 | 0.045 | |
| sample_annotation_to_colors | 0.035 | 0.004 | 0.039 | |