Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:32 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
To the developers/maintainers of the TBSignatureProfiler package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2012/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TBSignatureProfiler 1.11.0 (landing page) Aubrey R. Odom-Mabey
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: TBSignatureProfiler |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TBSignatureProfiler_1.11.0.tar.gz |
StartedAt: 2023-02-07 17:24:12 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 17:28:39 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 266.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: TBSignatureProfiler.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TBSignatureProfiler_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TBSignatureProfiler.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK * this is package ‘TBSignatureProfiler’ version ‘1.11.0’ * 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 ... ERROR Running examples in ‘TBSignatureProfiler-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: signatureGeneHeatmap > ### Title: Plot a heatmap of a single signature score with individual gene > ### expression levels. > ### Aliases: signatureGeneHeatmap > > ### ** Examples > > library(SummarizedExperiment) Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians > # Generate some artificial data that shows a difference in Zak_RISK_16 > mat_testdata <- rbind(matrix(c(rnorm(80), rnorm(80) + 5), 16, 10, + dimnames = list(TBsignatures$Zak_RISK_16, + paste0("sample", seq_len(10)))), + matrix(rnorm(1000), 100, 10, + dimnames = list(paste0("gene", seq_len(100)), + paste0("sample", seq_len(10))))) > > # Create a SummarizedExperiment object that contains the data > testdataSE <- SummarizedExperiment(assays = SimpleList(data = mat_testdata), + colData = DataFrame(sample = + c(rep("down", 5), + rep("up", 5)))) > # Run profiler using GSVA and ssGSEA on Zak_RISK_16 > res <- runTBsigProfiler(testdataSE, useAssay = "data", + signatures = TBsignatures["Zak_RISK_16"], + algorithm = c("GSVA", "ssGSEA"), parallel.sz = 1, + combineSigAndAlgorithm = TRUE) Parameter update_genes is TRUE. Gene names will be updated. Running GSVA Estimating GSVA scores for 1 gene sets. Estimating ECDFs with Gaussian kernels | | | 0% | |======================================================================| 100% Running ssGSEA 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..." > > # Plot a heatmap of signature genes and pathway predictions > signatureGeneHeatmap(res, useAssay = "data", + sigGenes = TBsignatures[["Zak_RISK_16"]], + signatureColNames = c("GSVA_Zak_RISK_16", + "ssGSEA_Zak_RISK_16"), + annotationColNames = c("sample"), showColumnNames = FALSE, + name = "Zak_RISK_16") Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘packagecoverage.R’ Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Backtrace: ▆ 1. └─testthat::expect_output(...) at test-bootstrap.R:48:2 2. └─testthat:::quasi_capture(...) 3. ├─testthat (local) .capture(...) 4. │ └─testthat::capture_output_lines(code, print, width = width) 5. │ └─testthat:::eval_with_output(code, print = print, width = width) 6. │ ├─withr::with_output_sink(path, withVisible(code)) 7. │ │ └─base::force(code) 8. │ └─base::withVisible(code) 9. └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) [ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘tbspVignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘tbspVignette.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/TBSignatureProfiler.Rcheck/vign_test/TBSignatureProfiler/vignettes/tbspVignette_files/figure-html/all_sigs_heatmap-1.png" but not available. Killed * checking PDF version of manual ... OK * DONE Status: 3 ERRORs See ‘/home/biocbuild/bbs-3.17-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’ for details.
TBSignatureProfiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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/packagecoverage.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > # 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 0.183 0.046 0.217
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 0.192 0.045 0.249
TBSignatureProfiler.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 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..." | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 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 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 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 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% | |======= | 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 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% | |======= | 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. [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% | |======= | 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% 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% | |======= | 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 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 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% [ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-bootstrap.R:48'): Run tableAUC ───────────────────────────────── Error in `tableAUC(SE_scored = scored_testdata, signatureColNames = "sig1", annotationColName = "Disease", pROC = FALSE, num.boot = 5)`: unused argument (pROC = FALSE) Backtrace: ▆ 1. └─testthat::expect_output(...) at test-bootstrap.R:48:2 2. └─testthat:::quasi_capture(...) 3. ├─testthat (local) .capture(...) 4. │ └─testthat::capture_output_lines(code, print, width = width) 5. │ └─testthat:::eval_with_output(code, print = print, width = width) 6. │ ├─withr::with_output_sink(path, withVisible(code)) 7. │ │ └─base::force(code) 8. │ └─base::withVisible(code) 9. └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) [ FAIL 1 | WARN 3 | SKIP 0 | PASS 141 ] Error: Test failures Execution halted
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
name | user | system | elapsed | |
COVIDsignatures | 0.024 | 0.000 | 0.024 | |
OriginalTrainingData | 0.001 | 0.000 | 0.001 | |
SignatureQuantitative | 4.621 | 0.205 | 6.042 | |
TBSPapp | 0.000 | 0.000 | 0.001 | |
TB_hiv | 0.001 | 0.001 | 0.001 | |
TB_indian | 0.000 | 0.001 | 0.000 | |
TBcommon | 0.000 | 0.001 | 0.001 | |
TBsignatures | 0.001 | 0.000 | 0.001 | |
TBsignaturesSplit | 0.001 | 0.000 | 0.001 | |
addTBsignature | 0.007 | 0.004 | 0.010 | |
bootstrapAUC | 12.780 | 0.368 | 14.187 | |
common_sigAnnotData | 0.000 | 0.001 | 0.001 | |
compareAlgs | 2.075 | 0.098 | 2.760 | |
compareBoxplots | 1.200 | 0.020 | 1.301 | |
deseq2_norm_rle | 0.305 | 0.000 | 0.371 | |
distinctColors | 0.001 | 0.000 | 0.001 | |
evaluateOriginalModel | 0.308 | 0.008 | 0.318 | |
mkAssay | 3.598 | 0.008 | 4.043 | |
plotQuantitative | 2.506 | 0.107 | 3.088 | |
runTBsigProfiler | 0.422 | 0.014 | 0.436 | |
sigAnnotData | 0.000 | 0.002 | 0.006 | |
signatureBoxplot | 1.082 | 0.016 | 1.157 | |