| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-03 02:36:28 -0000 (Fri, 03 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" | 4039 |
| 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: 2023-02-02 22:09:25 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 22:14:31 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 305.6 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bootstrapAUC 12.781 0.296 14.518
signatureROCplot_CI 8.705 0.032 9.632
signatureGeneHeatmap 5.136 0.004 5.501
SignatureQuantitative 4.678 0.096 5.890
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
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
0.199 0.032 0.261
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
0.223 0.014 0.452
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")
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[ 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 | 0.015 | 0.008 | 0.023 | |
| OriginalTrainingData | 0.001 | 0.000 | 0.001 | |
| SignatureQuantitative | 4.678 | 0.096 | 5.890 | |
| TBSPapp | 0.000 | 0.000 | 0.001 | |
| TB_hiv | 0.001 | 0.000 | 0.001 | |
| TB_indian | 0.001 | 0.000 | 0.001 | |
| TBcommon | 0.000 | 0.000 | 0.001 | |
| TBsignatures | 0.001 | 0.000 | 0.000 | |
| TBsignaturesSplit | 0.001 | 0.000 | 0.001 | |
| addTBsignature | 0.01 | 0.00 | 0.01 | |
| bootstrapAUC | 12.781 | 0.296 | 14.518 | |
| common_sigAnnotData | 0.001 | 0.000 | 0.001 | |
| compareAlgs | 2.006 | 0.100 | 2.223 | |
| compareBoxplots | 1.189 | 0.004 | 1.370 | |
| deseq2_norm_rle | 0.294 | 0.000 | 0.294 | |
| distinctColors | 0.001 | 0.000 | 0.001 | |
| evaluateOriginalModel | 0.302 | 0.016 | 0.319 | |
| mkAssay | 3.525 | 0.040 | 4.046 | |
| plotQuantitative | 2.438 | 0.071 | 2.975 | |
| runTBsigProfiler | 0.431 | 0.000 | 0.431 | |
| sigAnnotData | 0.000 | 0.001 | 0.001 | |
| signatureBoxplot | 1.022 | 0.014 | 1.062 | |
| signatureGeneHeatmap | 5.136 | 0.004 | 5.501 | |
| signatureHeatmap | 0.937 | 0.004 | 0.966 | |
| signatureROCplot | 1.011 | 0.015 | 1.059 | |
| signatureROCplot_CI | 8.705 | 0.032 | 9.632 | |
| tableAUC | 0.835 | 0.012 | 0.962 | |