David Jenkins
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TBSignatureProfiler |
| Branch: RELEASE_3_11 |
| Last Commit: 67171e1 |
| Last Changed Date: 2020-04-27 15:36:15 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:46 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TBSignatureProfiler PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1782/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TBSignatureProfiler 1.0.0 David Jenkins
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TBSignatureProfiler |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TBSignatureProfiler_1.0.0.tar.gz |
| StartedAt: 2020-10-17 05:49:38 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:54:07 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 268.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TBSignatureProfiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TBSignatureProfiler_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ 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 ‘TBSignatureProfiler’ 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 (user + system) or elapsed time > 5s
user system elapsed
bootstrapAUC 8.795 0.240 9.041
SignatureQuantitative 8.127 0.214 8.345
compareAlgs 7.600 0.340 7.949
signatureROCplot_CI 7.176 0.675 7.855
signatureGeneHeatmap 6.053 0.029 6.085
* 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
TBSignatureProfiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘TBSignatureProfiler’ ... ** 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 (TBSignatureProfiler)
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
0.309 0.074 0.360
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(TBSignatureProfiler)
>
> test_check("TBSignatureProfiler")
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 130 | SKIPPED: 1 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
78.254 2.934 81.242
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| SignatureQuantitative | 8.127 | 0.214 | 8.345 | |
| TBSPapp | 0.001 | 0.000 | 0.000 | |
| TB_hiv | 0.004 | 0.001 | 0.005 | |
| TB_indian | 0.001 | 0.001 | 0.003 | |
| TBcommon | 0.002 | 0.001 | 0.003 | |
| TBsignatures | 0.002 | 0.001 | 0.003 | |
| bootstrapAUC | 8.795 | 0.240 | 9.041 | |
| common_sigAnnotData | 0.002 | 0.001 | 0.003 | |
| compareAlgs | 7.600 | 0.340 | 7.949 | |
| compareBoxplots | 0.892 | 0.014 | 0.907 | |
| deseq2_norm_rle | 0.566 | 0.042 | 0.609 | |
| distinctColors | 0.001 | 0.000 | 0.002 | |
| mkAssay | 3.200 | 0.223 | 3.430 | |
| plotQuantitative | 3.931 | 0.068 | 4.002 | |
| runTBsigProfiler | 0.135 | 0.008 | 0.170 | |
| sigAnnotData | 0.002 | 0.002 | 0.003 | |
| signatureBoxplot | 0.958 | 0.018 | 0.983 | |
| signatureGeneHeatmap | 6.053 | 0.029 | 6.085 | |
| signatureHeatmap | 0.804 | 0.017 | 0.822 | |
| signatureROCplot | 0.593 | 0.004 | 0.598 | |
| signatureROCplot_CI | 7.176 | 0.675 | 7.855 | |
| tableAUC | 0.670 | 0.026 | 0.700 | |