David Jenkins
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/TBSignatureProfiler |
| Branch: RELEASE_3_12 |
| Last Commit: 16ccdd3 |
| Last Changed Date: 2020-10-27 11:56:28 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:37:08 -0400 (Thu, 06 May 2021).
|
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 1840/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.2.0 (landing page) David Jenkins
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TBSignatureProfiler |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2021-05-06 06:47:17 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:51:21 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 243.7 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.2.0’
* 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
compareAlgs 8.236 0.408 8.657
bootstrapAUC 8.052 0.196 8.281
signatureROCplot_CI 7.363 0.508 7.881
SignatureQuantitative 5.897 0.162 6.065
signatureGeneHeatmap 5.795 0.036 5.841
* 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 4.0.5 (2021-03-31) -- "Shake and Throw"
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
0.280 0.067 0.323
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(TBSignatureProfiler)
>
> test_check("TBSignatureProfiler")
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══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)
[ FAIL 0 | WARN 4 | SKIP 1 | PASS 130 ]
>
> proc.time()
user system elapsed
72.532 2.362 74.986
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| SignatureQuantitative | 5.897 | 0.162 | 6.065 | |
| TBSPapp | 0.001 | 0.000 | 0.000 | |
| TB_hiv | 0.003 | 0.002 | 0.004 | |
| TB_indian | 0.001 | 0.001 | 0.002 | |
| TBcommon | 0.001 | 0.001 | 0.002 | |
| TBsignatures | 0.001 | 0.002 | 0.003 | |
| bootstrapAUC | 8.052 | 0.196 | 8.281 | |
| common_sigAnnotData | 0.001 | 0.001 | 0.002 | |
| compareAlgs | 8.236 | 0.408 | 8.657 | |
| compareBoxplots | 1.373 | 0.037 | 1.412 | |
| deseq2_norm_rle | 0.424 | 0.022 | 0.447 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| mkAssay | 2.206 | 0.183 | 2.393 | |
| plotQuantitative | 3.082 | 0.014 | 3.099 | |
| runTBsigProfiler | 0.310 | 0.003 | 0.314 | |
| sigAnnotData | 0.001 | 0.000 | 0.001 | |
| signatureBoxplot | 1.013 | 0.019 | 1.034 | |
| signatureGeneHeatmap | 5.795 | 0.036 | 5.841 | |
| signatureHeatmap | 1.684 | 0.027 | 1.714 | |
| signatureROCplot | 1.117 | 0.007 | 1.126 | |
| signatureROCplot_CI | 7.363 | 0.508 | 7.881 | |
| tableAUC | 1.314 | 0.054 | 1.371 | |