Aubrey R. Odom
| Snapshot Date: 2024-08-26 14:00 -0400 (Mon, 26 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/TBSignatureProfiler |
| git_branch: devel |
| git_last_commit: d4c61d3 |
| git_last_commit_date: 2024-05-07 11:29:04 -0400 (Tue, 07 May 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2092/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.17.1 (landing page) Aubrey R. Odom
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the TBSignatureProfiler package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TBSignatureProfiler.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: TBSignatureProfiler |
| Version: 1.17.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TBSignatureProfiler_1.17.1.tar.gz |
| StartedAt: 2024-08-27 09:47:39 -0000 (Tue, 27 Aug 2024) |
| EndedAt: 2024-08-27 09:50:52 -0000 (Tue, 27 Aug 2024) |
| EllapsedTime: 193.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TBSignatureProfiler.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TBSignatureProfiler_1.17.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.17.1’
* 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 code 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bootstrapAUC 13.774 0.467 14.282
signatureROCplot_CI 7.315 0.036 7.367
signatureGeneHeatmap 6.706 0.079 6.803
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘packagecoverage.R’
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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/packagecoverage.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
> # Coverage Script
> # Run tests and generate Code Coverage Report
>
> # Look at a specific script ---------------------------------------------------
> #test_for_me <- function(codefile, testfile) {
> # test_file(testfile)
> # res <- covr::file_coverage(codefile, testfile)
> # print(res)
> # covr::report(res)
> #}
>
> #test_for_me("R/evaluate.R", "tests/testthat/test-evaluate.R")
> # Look at whole package -------------------------------------------------------
> # Gets percent coverage for entire package, by script
> #covr::package_coverage()
> #
> # Report with gui (probably the best here)
> #covr::report()
>
> proc.time()
user system elapsed
0.184 0.037 0.207
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.200 0.026 0.211
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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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================================================================================
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ]
>
> proc.time()
user system elapsed
80.161 1.302 81.593
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| COVIDsignatures | 0.018 | 0.004 | 0.022 | |
| OriginalTrainingData | 0.000 | 0.000 | 0.001 | |
| SignatureQuantitative | 4.307 | 0.094 | 4.494 | |
| TBSPapp | 0 | 0 | 0 | |
| TB_hiv | 0.001 | 0.000 | 0.001 | |
| TB_indian | 0.001 | 0.000 | 0.001 | |
| TBcommon | 0.001 | 0.000 | 0.001 | |
| TBsignatures | 0.000 | 0.000 | 0.001 | |
| TBsignaturesSplit | 0 | 0 | 0 | |
| addTBsignature | 0.009 | 0.000 | 0.009 | |
| bootstrapAUC | 13.774 | 0.467 | 14.282 | |
| common_sigAnnotData | 0.001 | 0.000 | 0.001 | |
| compareAlgs | 3.228 | 0.112 | 3.346 | |
| compareBoxplots | 1.145 | 0.068 | 1.216 | |
| deseq2_norm_rle | 0.328 | 0.000 | 0.329 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| evaluateOriginalModel | 0.357 | 0.012 | 0.369 | |
| mkAssay | 3.664 | 0.068 | 3.740 | |
| plotQuantitative | 2.073 | 0.048 | 2.126 | |
| runTBsigProfiler | 0.782 | 0.012 | 0.797 | |
| sigAnnotData | 0.001 | 0.000 | 0.001 | |
| signatureBoxplot | 1.191 | 0.036 | 1.229 | |
| signatureGeneHeatmap | 6.706 | 0.079 | 6.803 | |
| signatureHeatmap | 1.062 | 0.008 | 1.072 | |
| signatureROCplot | 1.132 | 0.004 | 1.138 | |
| signatureROCplot_CI | 7.315 | 0.036 | 7.367 | |
| tableAUC | 0.793 | 0.016 | 0.811 | |