| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 2025/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TBSignatureProfiler 1.10.0 (landing page) Aubrey R. Odom-Mabey
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TBSignatureProfiler |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TBSignatureProfiler_1.10.0.tar.gz |
| StartedAt: 2023-04-11 00:29:53 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:33:06 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 193.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TBSignatureProfiler.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TBSignatureProfiler.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TBSignatureProfiler_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TBSignatureProfiler.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TBSignatureProfiler/DESCRIPTION’ ... OK
* this is package ‘TBSignatureProfiler’ version ‘1.10.0’
* 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 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 9.574 0.496 10.075
* 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:
1. ├─testthat::expect_is(...) at test-evaluate.R:30:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TBSignatureProfiler:::Bootstrap_LOOCV_LR_AUC(...)
5. ├─base::suppressWarnings(...)
6. │ └─base::withCallingHandlers(...)
7. └─TBSignatureProfiler:::LOOAUC_simple_multiple_noplot_one_df(...)
8. ├─base::suppressWarnings(glmnet::glmnet(train, targetVec[-j], family = "binomial"))
9. │ └─base::withCallingHandlers(...)
10. └─glmnet::glmnet(train, targetVec[-j], family = "binomial")
11. └─glmnet:::lognet(...)
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 143 ]
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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.16-bioc/meat/TBSignatureProfiler.Rcheck/00check.log’
for details.
TBSignatureProfiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TBSignatureProfiler ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.
> # 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
0.161 0.024 0.167
TBSignatureProfiler.Rcheck/tests/spelling.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
0.151 0.039 0.174
TBSignatureProfiler.Rcheck/tests/testthat.Rout.fail
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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")
|
| | 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%
|
| | 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 143 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-evaluate.R:30:3'): LOOAUC works ────────────────────────────────
Error in `lognet(xd, is.sparse, ix, jx, y, weights, offset, alpha, nobs,
nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd,
intr, vnames, maxit, kopt, family, pb)`: one multinomial or binomial class has 1 or 0 observations; not allowed
Backtrace:
▆
1. ├─testthat::expect_is(...) at test-evaluate.R:30:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─TBSignatureProfiler:::Bootstrap_LOOCV_LR_AUC(...)
5. ├─base::suppressWarnings(...)
6. │ └─base::withCallingHandlers(...)
7. └─TBSignatureProfiler:::LOOAUC_simple_multiple_noplot_one_df(...)
8. ├─base::suppressWarnings(glmnet::glmnet(train, targetVec[-j], family = "binomial"))
9. │ └─base::withCallingHandlers(...)
10. └─glmnet::glmnet(train, targetVec[-j], family = "binomial")
11. └─glmnet:::lognet(...)
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 143 ]
Error: Test failures
Execution halted
TBSignatureProfiler.Rcheck/TBSignatureProfiler-Ex.timings
| name | user | system | elapsed | |
| COVIDsignatures | 0.023 | 0.000 | 0.023 | |
| OriginalTrainingData | 0.001 | 0.000 | 0.000 | |
| SignatureQuantitative | 3.419 | 0.163 | 3.592 | |
| TBSPapp | 0 | 0 | 0 | |
| TB_hiv | 0.001 | 0.000 | 0.001 | |
| TB_indian | 0.001 | 0.000 | 0.000 | |
| TBcommon | 0.001 | 0.000 | 0.000 | |
| TBsignatures | 0.001 | 0.000 | 0.000 | |
| TBsignaturesSplit | 0.001 | 0.000 | 0.000 | |
| addTBsignature | 0.005 | 0.004 | 0.010 | |
| bootstrapAUC | 9.574 | 0.496 | 10.075 | |
| common_sigAnnotData | 0.001 | 0.000 | 0.000 | |
| compareAlgs | 2.252 | 0.144 | 2.396 | |
| compareBoxplots | 0.836 | 0.020 | 0.855 | |
| deseq2_norm_rle | 0.31 | 0.00 | 0.31 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| evaluateOriginalModel | 0.176 | 0.004 | 0.180 | |
| mkAssay | 2.67 | 0.10 | 2.77 | |
| plotQuantitative | 2.515 | 0.052 | 2.567 | |
| runTBsigProfiler | 0.250 | 0.008 | 0.258 | |
| sigAnnotData | 0.001 | 0.000 | 0.001 | |
| signatureBoxplot | 0.719 | 0.012 | 0.731 | |
| signatureGeneHeatmap | 3.232 | 0.048 | 3.280 | |
| signatureHeatmap | 0.654 | 0.000 | 0.654 | |
| signatureROCplot | 0.632 | 0.004 | 0.636 | |
| signatureROCplot_CI | 4.561 | 0.036 | 4.597 | |
| tableAUC | 0.571 | 0.020 | 0.592 | |