Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:29:24 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TBSignatureProfiler_1.2.0.tar.gz |
StartedAt: 2021-05-06 06:34:37 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 06:38:22 -0400 (Thu, 06 May 2021) |
EllapsedTime: 225.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TBSignatureProfiler.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TBSignatureProfiler_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/TBSignatureProfiler.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (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 bootstrapAUC 8.540 0.104 8.659 compareAlgs 7.080 0.196 7.290 SignatureQuantitative 6.172 0.200 6.404 signatureROCplot_CI 6.156 0.000 6.177 signatureGeneHeatmap 5.316 0.000 5.324 * 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: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-pc-linux-gnu (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 0.152 0.020 0.171
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-pc-linux-gnu (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") Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating GSVA scores for 1 gene sets. 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Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating PLAGE scores for 1 gene sets. | | | 0% | |======================================================================| 100% 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% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating ssGSEA scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% ================================================================================ ================================================================================ 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% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% Estimating combined z-scores for 1 gene sets. | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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% ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On CRAN (1) [ FAIL 0 | WARN 4 | SKIP 1 | PASS 130 ] > > proc.time() user system elapsed 67.228 0.724 68.197
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
name | user | system | elapsed | |
SignatureQuantitative | 6.172 | 0.200 | 6.404 | |
TBSPapp | 0.000 | 0.000 | 0.001 | |
TB_hiv | 0.004 | 0.000 | 0.003 | |
TB_indian | 0.004 | 0.000 | 0.001 | |
TBcommon | 0.000 | 0.000 | 0.001 | |
TBsignatures | 0.004 | 0.000 | 0.001 | |
bootstrapAUC | 8.540 | 0.104 | 8.659 | |
common_sigAnnotData | 0.004 | 0.000 | 0.001 | |
compareAlgs | 7.080 | 0.196 | 7.290 | |
compareBoxplots | 1.636 | 0.012 | 1.650 | |
deseq2_norm_rle | 0.440 | 0.000 | 0.442 | |
distinctColors | 0.000 | 0.000 | 0.001 | |
mkAssay | 2.624 | 0.020 | 2.648 | |
plotQuantitative | 2.840 | 0.000 | 2.847 | |
runTBsigProfiler | 0.252 | 0.000 | 0.249 | |
sigAnnotData | 0.000 | 0.000 | 0.001 | |
signatureBoxplot | 0.936 | 0.000 | 0.936 | |
signatureGeneHeatmap | 5.316 | 0.000 | 5.324 | |
signatureHeatmap | 2.104 | 0.004 | 2.115 | |
signatureROCplot | 1.324 | 0.004 | 1.333 | |
signatureROCplot_CI | 6.156 | 0.000 | 6.177 | |
tableAUC | 1.068 | 0.016 | 1.085 | |