| Back to Build/check report for BioC 3.17 |
|
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 | |