Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:56 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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 2110/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TBSignatureProfiler 1.14.0 (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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-03-03 23:53:26 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 23:56:23 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 177.2 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/TBSignatureProfiler.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK * this is package ‘TBSignatureProfiler’ version ‘1.14.0’ * 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 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 12.164 0.756 13.002 signatureROCplot_CI 5.915 0.407 6.371 * 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 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/Resources/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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. > # 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 0.206 0.077 0.272
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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 0.210 0.076 0.275
TBSignatureProfiler.Rcheck/tests/testthat.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." 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[1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. 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[1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." ================================================================================ Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." 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Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." ================================================================================ Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." ================================================================================ Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." Estimating ssGSEA scores for 1 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% [1] "Normalizing..." ================================================================================ ================================================================================ Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% [ FAIL 0 | WARN 49 | SKIP 0 | PASS 136 ] [ FAIL 0 | WARN 49 | SKIP 0 | PASS 136 ] > > proc.time() user system elapsed 61.092 3.573 65.024
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
name | user | system | elapsed | |
COVIDsignatures | 0.018 | 0.005 | 0.023 | |
OriginalTrainingData | 0.001 | 0.002 | 0.002 | |
SignatureQuantitative | 3.664 | 0.227 | 3.912 | |
TBSPapp | 0 | 0 | 0 | |
TB_hiv | 0.001 | 0.002 | 0.003 | |
TB_indian | 0.001 | 0.002 | 0.002 | |
TBcommon | 0.001 | 0.001 | 0.002 | |
TBsignatures | 0.001 | 0.001 | 0.002 | |
TBsignaturesSplit | 0.001 | 0.001 | 0.002 | |
addTBsignature | 0.009 | 0.003 | 0.012 | |
bootstrapAUC | 12.164 | 0.756 | 13.002 | |
common_sigAnnotData | 0.000 | 0.001 | 0.002 | |
compareAlgs | 2.795 | 0.169 | 2.990 | |
compareBoxplots | 1.079 | 0.140 | 1.319 | |
deseq2_norm_rle | 0.309 | 0.039 | 0.351 | |
distinctColors | 0.001 | 0.000 | 0.005 | |
evaluateOriginalModel | 0.210 | 0.011 | 0.221 | |
mkAssay | 3.139 | 0.226 | 3.395 | |
plotQuantitative | 1.839 | 0.051 | 1.905 | |
runTBsigProfiler | 0.369 | 0.019 | 0.395 | |
sigAnnotData | 0.001 | 0.002 | 0.003 | |
signatureBoxplot | 1.018 | 0.032 | 1.068 | |
signatureGeneHeatmap | 4.337 | 0.078 | 4.455 | |
signatureHeatmap | 0.837 | 0.026 | 0.870 | |
signatureROCplot | 0.870 | 0.017 | 0.895 | |
signatureROCplot_CI | 5.915 | 0.407 | 6.371 | |
tableAUC | 0.698 | 0.060 | 0.765 | |