Stevie Pederson
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ngsReports |
| git_branch: RELEASE_3_21 |
| git_last_commit: 2ccdba7 |
| git_last_commit_date: 2025-09-16 08:46:25 -0400 (Tue, 16 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 | ||||
| Package 1445/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ngsReports 2.10.1 (landing page) Stevie Pederson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the ngsReports package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ngsReports.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ngsReports |
| Version: 2.10.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ngsReports_2.10.1.tar.gz |
| StartedAt: 2025-10-14 11:58:53 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 12:03:41 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 288.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ngsReports.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ngsReports_2.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ngsReports.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ngsReports/DESCRIPTION’ ... OK
* this is package ‘ngsReports’ version ‘2.10.1’
* 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 ‘ngsReports’ 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 code 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
plotSeqContent-methods 4.825 0.052 5.059
plotAdapterContent-methods 4.403 0.191 5.337
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
6. └─plotly:::ggplotly.ggplot(x, tooltip = hv)
7. └─plotly::gg2list(...)
── Error ('test-renderDendro.R:11:1'): (code run outside of `test_that()`) ─────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. └─ngsReports:::.renderDendro(dx$segments) at test-renderDendro.R:11:1
2. ├─plotly::ggplotly(dendro, tooltip = NULL)
3. └─plotly:::ggplotly.ggplot(dendro, tooltip = NULL)
4. └─plotly::gg2list(...)
[ FAIL 24 | WARN 0 | SKIP 0 | PASS 294 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ngsReports.Rcheck/00check.log’
for details.
ngsReports.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ngsReports ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘ngsReports’ ... ** this is package ‘ngsReports’ version ‘2.10.1’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (ngsReports)
ngsReports.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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(ngsReports)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: ggplot2
Loading required package: patchwork
Loading required package: tibble
>
> test_check("ngsReports")
[ FAIL 24 | WARN 0 | SKIP 0 | PASS 294 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-allPlots.R:5:3'): plotOverrep outputs correct objects ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotOverrep(fdl[[1]], TRUE) at test-allPlots.R:5:3
2. └─ngsReports::plotOverrep(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, pwfCols, ...)
4. ├─base::suppressMessages(suppressWarnings(plotly::ggplotly(p)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressWarnings(plotly::ggplotly(p))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p)
9. └─plotly:::ggplotly.ggplot(p)
10. └─plotly::gg2list(...)
── Error ('test-allPlots.R:38:3'): plotSeqLengthDistn outputs correct objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotSeqLengthDistn(fdl[[1]], TRUE) at test-allPlots.R:38:3
2. └─ngsReports::plotSeqLengthDistn(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(plotly::ggplotly(p, tooltip = c("x", "y")))
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(p, tooltip = c("x", "y"))
7. └─plotly:::ggplotly.ggplot(p, tooltip = c("x", "y"))
8. └─plotly::gg2list(...)
── Error ('test-allPlots.R:72:3'): plotSeqQuals outputs correct objects ────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotSeqQuals(fdl[[1]], TRUE) at test-allPlots.R:72:3
2. └─ngsReports::plotSeqQuals(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, pwfCols, ...)
4. ├─base::suppressMessages(suppressWarnings(plotly::ggplotly(p, hoverinfo = hv)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressWarnings(plotly::ggplotly(p, hoverinfo = hv))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p, hoverinfo = hv)
9. └─plotly:::ggplotly.ggplot(p, hoverinfo = hv)
10. └─plotly::gg2list(...)
── Error ('test-makeSidebar.R:5:1'): (code run outside of `test_that()`) ───────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. └─ngsReports:::.makeSidebar(status, key, pwf) at test-makeSidebar.R:5:1
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. ├─base::suppressMessages(...)
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(sideBar, tooltip = c("y", "fill"))
7. └─plotly:::ggplotly.ggplot(sideBar, tooltip = c("y", "fill"))
8. └─plotly::gg2list(...)
── Error ('test-plotAdapterContent.R:7:3'): plotAdapterContent outputs correct object classes ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotAdapterContent(fdl[[1]], TRUE) at test-plotAdapterContent.R:7:3
2. └─ngsReports::plotAdapterContent(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressWarnings(suppressMessages(plotly::ggplotly(p)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressMessages(plotly::ggplotly(p))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p)
9. └─plotly:::ggplotly.ggplot(p)
10. └─plotly::gg2list(...)
── Error ('test-plotAdapterContent.R:34:3'): FastpData plots correctly ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotAdapterContent(fp, TRUE) at test-plotAdapterContent.R:34:3
2. └─ngsReports::plotAdapterContent(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(plotly::ggplotly(p, tooltip = hv))
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(p, tooltip = hv)
7. └─plotly:::ggplotly.ggplot(p, tooltip = hv)
8. └─plotly::gg2list(...)
── Error ('test-plotAdapterContent.R:47:3'): FastpDataList plots correctly ─────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotAdapterContent(...) at test-plotAdapterContent.R:47:3
2. └─ngsReports::plotAdapterContent(...)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. └─ngsReports:::.prepHeatmap(...)
5. └─ngsReports:::.makeSidebar(...)
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. ├─base::suppressMessages(...)
9. │ └─base::withCallingHandlers(...)
10. ├─plotly::ggplotly(sideBar, tooltip = c("y", "fill"))
11. └─plotly:::ggplotly.ggplot(sideBar, tooltip = c("y", "fill"))
12. └─plotly::gg2list(...)
── Error ('test-plotBaseQuals.R:7:3'): plotBaseQuals (FastQC) outputs correct objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotBaseQuals(fdl[[1]], TRUE) at test-plotBaseQuals.R:7:3
2. └─ngsReports::plotBaseQuals(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(suppressWarnings(plotly::ggplotly(p, tooltip = hv)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressWarnings(plotly::ggplotly(p, tooltip = hv))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p, tooltip = hv)
9. └─plotly:::ggplotly.ggplot(p, tooltip = hv)
10. └─plotly::gg2list(...)
── Error ('test-plotBaseQuals.R:30:3'): plotBaseQuals (Fastp) output correct objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotBaseQuals(fp, TRUE) at test-plotBaseQuals.R:30:3
2. └─ngsReports::plotBaseQuals(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(suppressWarnings(plotly::ggplotly(p, tooltip = tt)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressWarnings(plotly::ggplotly(p, tooltip = tt))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p, tooltip = tt)
9. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
10. └─plotly::gg2list(...)
── Error ('test-plotDupLevels.R:6:3'): plotDupLevels outputs correct objects from FastQC ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotDupLevels(fdl[[1]], TRUE) at test-plotDupLevels.R:6:3
2. └─ngsReports::plotDupLevels(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(plotly::ggplotly(p, tooltip = tt))
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(p, tooltip = tt)
7. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
8. └─plotly::gg2list(...)
── Error ('test-plotDupLevels.R:28:3'): plotDupLevels fastp outputs are correct ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotDupLevels(fp, TRUE) at test-plotDupLevels.R:28:3
2. └─ngsReports::plotDupLevels(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = tt)
5. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
6. └─plotly::gg2list(...)
── Error ('test-plotGcContent.R:7:3'): plotGcContent outputs correct objects ───
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotGcContent(fdl[[1]], usePlotly = TRUE) at test-plotGcContent.R:7:3
2. └─ngsReports::plotGcContent(fdl[[1]], usePlotly = TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressWarnings(suppressMessages(plotly::ggplotly(p, tooltip = ttip)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressMessages(plotly::ggplotly(p, tooltip = ttip))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p, tooltip = ttip)
9. └─plotly:::ggplotly.ggplot(p, tooltip = ttip)
10. └─plotly::gg2list(...)
── Error ('test-plotGcContent.R:40:3'): plotGcContent works for Fastp structures ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotGcContent(fpl[[1]], usePlotly = TRUE) at test-plotGcContent.R:40:3
2. └─ngsReports::plotGcContent(fpl[[1]], usePlotly = TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = hv)
5. └─plotly:::ggplotly.ggplot(p, tooltip = hv)
6. └─plotly::gg2list(...)
── Error ('test-plotInsertSize.R:7:3'): Basic FastpData Plots work ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotInsertSize(fp, TRUE) at test-plotInsertSize.R:7:3
2. └─ngsReports::plotInsertSize(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = tt)
5. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
6. └─plotly::gg2list(...)
── Error ('test-plotInsertSize.R:25:3'): Basic FastpDataList Plots work ────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotInsertSize(fp, TRUE) at test-plotInsertSize.R:25:3
2. └─ngsReports::plotInsertSize(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = tt)
5. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
6. └─plotly::gg2list(...)
── Error ('test-plotKmers.R:6:3'): plotKmers outputs correct objects ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotKmers(fdl[[1]], TRUE) at test-plotKmers.R:6:3
2. └─ngsReports::plotKmers(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p)
5. └─plotly:::ggplotly.ggplot(p)
6. └─plotly::gg2list(...)
── Error ('test-plotKmers.R:25:3'): FastpData objects plot correctly ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotKmers(fp, TRUE) at test-plotKmers.R:25:3
2. └─ngsReports::plotKmers(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressWarnings(plotly::ggplotly(p, tooltip = hv))
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(p, tooltip = hv)
7. └─plotly:::ggplotly.ggplot(p, tooltip = hv)
8. └─plotly::gg2list(...)
── Error ('test-plotNContent.R:19:3'): plotNContent works for all variations of FastpData params ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotNContent(fp, TRUE) at test-plotNContent.R:19:3
2. └─ngsReports::plotNContent(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressWarnings(plotly::ggplotly(p, tooltip = hv))
5. │ └─base::withCallingHandlers(...)
6. ├─plotly::ggplotly(p, tooltip = hv)
7. └─plotly:::ggplotly.ggplot(p, tooltip = hv)
8. └─plotly::gg2list(...)
── Error ('test-plotReadTotals.R:7:3'): plotReadTotals works for FastQC objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotReadTotals(fdl, usePlotly = TRUE) at test-plotReadTotals.R:7:3
2. └─ngsReports::plotReadTotals(fdl, usePlotly = TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─base::suppressMessages(suppressWarnings(plotly::ggplotly(p)))
5. │ └─base::withCallingHandlers(...)
6. ├─base::suppressWarnings(plotly::ggplotly(p))
7. │ └─base::withCallingHandlers(...)
8. ├─plotly::ggplotly(p)
9. └─plotly:::ggplotly.ggplot(p)
10. └─plotly::gg2list(...)
── Error ('test-plotReadTotals.R:16:3'): plotReadtTotals works for Fastp objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotReadTotals(fpl, usePlotly = TRUE) at test-plotReadTotals.R:16:3
2. └─ngsReports::plotReadTotals(fpl, usePlotly = TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = tt)
5. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
6. └─plotly::gg2list(...)
── Error ('test-plotSeqContent.R:6:3'): plotSeqContent outputs correct objects ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotSeqContent(fdl[[1]], TRUE) at test-plotSeqContent.R:6:3
2. └─ngsReports::plotSeqContent(fdl[[1]], TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = ttip)
5. └─plotly:::ggplotly.ggplot(p, tooltip = ttip)
6. └─plotly::gg2list(...)
── Error ('test-plotSeqContent.R:29:3'): plotSeqContent(FastpData) works ───────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotSeqContent(fp, TRUE) at test-plotSeqContent.R:29:3
2. └─ngsReports::plotSeqContent(fp, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. ├─plotly::ggplotly(p, tooltip = tt)
5. └─plotly:::ggplotly.ggplot(p, tooltip = tt)
6. └─plotly::gg2list(...)
── Error ('test-plotSeqContent.R:42:3'): plotSeqContent(FastpDataList) works ───
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. ├─ngsReports::plotSeqContent(fpl, TRUE) at test-plotSeqContent.R:42:3
2. └─ngsReports::plotSeqContent(fpl, TRUE)
3. └─ngsReports (local) .local(x, usePlotly, labels, pattern, ...)
4. └─ngsReports:::.prepHeatmap(...)
5. ├─plotly::ggplotly(x, tooltip = hv)
6. └─plotly:::ggplotly.ggplot(x, tooltip = hv)
7. └─plotly::gg2list(...)
── Error ('test-renderDendro.R:11:1'): (code run outside of `test_that()`) ─────
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
▆
1. └─ngsReports:::.renderDendro(dx$segments) at test-renderDendro.R:11:1
2. ├─plotly::ggplotly(dendro, tooltip = NULL)
3. └─plotly:::ggplotly.ggplot(dendro, tooltip = NULL)
4. └─plotly::gg2list(...)
[ FAIL 24 | WARN 0 | SKIP 0 | PASS 294 ]
Error: Test failures
Execution halted
ngsReports.Rcheck/ngsReports-Ex.timings
| name | user | system | elapsed | |
| FastqcData | 0.094 | 0.004 | 0.230 | |
| FastqcDataList | 0.413 | 0.044 | 0.753 | |
| TheoreticalGC-class | 0.089 | 0.004 | 0.184 | |
| dot-FastqcFile-class | 0.002 | 0.000 | 0.007 | |
| dot-addPercent | 0 | 0 | 0 | |
| dot-emptyPlot | 0.292 | 0.000 | 0.402 | |
| dot-makeDendro | 0.541 | 0.000 | 0.546 | |
| dot-makeLabels | 0.001 | 0.000 | 0.001 | |
| dot-splitByTab | 0.004 | 0.000 | 0.004 | |
| estGcDistn | 0.027 | 0.000 | 0.028 | |
| extract-methods | 0.415 | 0.000 | 0.415 | |
| fqName-methods | 0.610 | 0.011 | 0.944 | |
| fqcVersion | 0.435 | 0.016 | 0.452 | |
| gcAvail | 0.027 | 0.000 | 0.027 | |
| gcTheoretical | 0.048 | 0.000 | 0.048 | |
| getColours-methods | 0.002 | 0.000 | 0.002 | |
| getGC | 0.024 | 0.000 | 0.023 | |
| getModule | 0.493 | 0.000 | 0.618 | |
| getSummary | 0.433 | 0.004 | 0.438 | |
| importNgsLogs | 0.026 | 0.004 | 0.064 | |
| importSJ | 0.008 | 0.000 | 0.014 | |
| isCompressed | 0.000 | 0.002 | 0.006 | |
| mData | 0.028 | 0.001 | 0.062 | |
| maxAdapterContent | 0.900 | 0.016 | 0.984 | |
| overRep2Fasta-methods | 0.436 | 0.020 | 0.458 | |
| path | 0.409 | 0.020 | 0.430 | |
| plotAdapterContent-methods | 4.403 | 0.191 | 5.337 | |
| plotAlignmentSummary | 0.510 | 0.000 | 0.565 | |
| plotAssemblyStats | 1.176 | 0.000 | 1.372 | |
| plotBaseQuals-methods | 2.628 | 0.036 | 2.993 | |
| plotDupLevels-methods | 1.890 | 0.003 | 2.405 | |
| plotFastqcPCA-methods | 0.933 | 0.008 | 1.038 | |
| plotGcContent-methods | 1.596 | 0.112 | 1.863 | |
| plotInsertSize-methods | 0.966 | 0.024 | 1.082 | |
| plotKmers-methods | 3.059 | 0.031 | 3.369 | |
| plotNContent-methods | 1.274 | 0.004 | 1.351 | |
| plotOverrep-methods | 1.251 | 0.000 | 1.626 | |
| plotReadTotals-methods | 1.161 | 0.008 | 1.309 | |
| plotSeqContent-methods | 4.825 | 0.052 | 5.059 | |
| plotSeqLengthDistn-methods | 1.899 | 0.000 | 2.408 | |
| plotSeqQuals-methods | 2.044 | 0.004 | 2.524 | |
| plotSummary-methods | 0.818 | 0.004 | 0.859 | |
| pwf | 0.005 | 0.000 | 0.004 | |
| readTotals | 0.446 | 0.000 | 0.447 | |
| summariseOverrep-methods | 0.750 | 0.008 | 0.820 | |
| writeHtmlReport | 0 | 0 | 0 | |