Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:31:58 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 2071/2233 | 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 | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: TBSignatureProfiler |
Version: 1.17.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.17.1.tar.gz |
StartedAt: 2024-05-31 16:36:28 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 16:41:50 -0400 (Fri, 31 May 2024) |
EllapsedTime: 321.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TBSignatureProfiler.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TBSignatureProfiler_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TBSignatureProfiler.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * 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 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 20.492 1.177 22.511 signatureROCplot_CI 10.286 0.442 11.150 signatureGeneHeatmap 9.667 0.172 10.053 SignatureQuantitative 7.193 0.362 7.762 compareAlgs 4.678 0.274 5.319 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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/packagecoverage.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 0.356 0.110 0.429
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 0.356 0.115 0.432
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." ================================================================================ [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." ================================================================================ [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." ================================================================================ [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." ================================================================================ ================================================================================ [ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 136 ] > > proc.time() user system elapsed 120.290 4.146 128.819
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
name | user | system | elapsed | |
COVIDsignatures | 0.029 | 0.006 | 0.037 | |
OriginalTrainingData | 0.001 | 0.003 | 0.004 | |
SignatureQuantitative | 7.193 | 0.362 | 7.762 | |
TBSPapp | 0.000 | 0.001 | 0.001 | |
TB_hiv | 0.002 | 0.002 | 0.003 | |
TB_indian | 0.001 | 0.002 | 0.004 | |
TBcommon | 0.002 | 0.003 | 0.004 | |
TBsignatures | 0.001 | 0.003 | 0.004 | |
TBsignaturesSplit | 0.002 | 0.003 | 0.004 | |
addTBsignature | 0.011 | 0.004 | 0.015 | |
bootstrapAUC | 20.492 | 1.177 | 22.511 | |
common_sigAnnotData | 0.002 | 0.002 | 0.004 | |
compareAlgs | 4.678 | 0.274 | 5.319 | |
compareBoxplots | 2.028 | 0.198 | 2.293 | |
deseq2_norm_rle | 0.618 | 0.022 | 0.661 | |
distinctColors | 0.001 | 0.000 | 0.002 | |
evaluateOriginalModel | 0.49 | 0.02 | 0.53 | |
mkAssay | 4.271 | 0.227 | 4.563 | |
plotQuantitative | 3.704 | 0.085 | 3.816 | |
runTBsigProfiler | 0.761 | 0.040 | 0.803 | |
sigAnnotData | 0.002 | 0.002 | 0.004 | |
signatureBoxplot | 1.839 | 0.033 | 1.885 | |
signatureGeneHeatmap | 9.667 | 0.172 | 10.053 | |
signatureHeatmap | 1.542 | 0.029 | 1.579 | |
signatureROCplot | 1.799 | 0.009 | 1.829 | |
signatureROCplot_CI | 10.286 | 0.442 | 11.150 | |
tableAUC | 1.323 | 0.067 | 1.458 | |