Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 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 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 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 461/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CRISPRball 1.4.0 (landing page) Jared Andrews
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the CRISPRball package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRISPRball.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: CRISPRball |
Version: 1.4.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CRISPRball.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CRISPRball_1.4.0.tar.gz |
StartedAt: 2025-10-10 07:39:52 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 07:46:08 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 376.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: CRISPRball.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CRISPRball.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CRISPRball_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRball.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 ‘CRISPRball/DESCRIPTION’ ... OK * this is package ‘CRISPRball’ version ‘1.4.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CRISPRball’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘CRISPRball-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_bar > ### Title: Create interactive bar plot > ### Aliases: plot_bar > > ### ** Examples > > library(CRISPRball) > count.summ <- read.delim(system.file("extdata", "escneg.countsummary.txt", + package = "CRISPRball" + ), check.names = FALSE) > # Gini Index plot > plot_bar(count.summ) Error in pm[[2]] : subscript out of bounds Calls: plot_bar ... %||% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list Execution halted <pool> Checked-out object deleted before being returned. <pool> Make sure to `poolReturn()` all objects retrieved with `poolCheckout().` Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_depmap_essentiality 2.823 0.184 7.087 * 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: 1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "Zerocounts") at test-plotting_qc.R:10:5 2. │ ├─... %>% ... 3. │ ├─plotly::ggplotly(gg, tooltip = c("y")) 4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y")) 5. │ └─plotly::gg2list(...) 6. ├─plotly::config(...) 7. │ └─plotly:::modify_list(p$x$config, args) 8. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) 9. │ │ └─base::stopifnot(is.list(x), is.list(val)) 10. │ └─x %||% list() 11. └─plotly::layout(...) [ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ] 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: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/CRISPRball.Rcheck/00check.log’ for details.
CRISPRball.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CRISPRball ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘CRISPRball’ ... ** this is package ‘CRISPRball’ version ‘1.4.0’ ** using staged installation ** R ** data ** 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 (CRISPRball)
CRISPRball.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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(CRISPRball) Loading required package: shinyBS > > test_check("CRISPRball") Loading required package: pool Loading required package: RSQLite -- removing the lower 10% of variables based on variance Loading required package: ggplot2 Attaching package: 'plotly' The following object is masked from 'package:ggplot2': last_plot The following object is masked from 'package:stats': filter The following object is masked from 'package:graphics': layout [ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plotting_depmap.R:143:5'): plot_depmap_dependency returns a plotly object ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df)) at test-plotting_depmap.R:143:5 2. │ └─base::withCallingHandlers(...) 3. ├─CRISPRball::plot_depmap_dependency(df) 4. │ ├─ggplotly(gg, tooltip = "text") %>% ... 5. │ ├─plotly::ggplotly(gg, tooltip = "text") 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 7. │ └─plotly::gg2list(...) 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density")) ── Error ('test-plotting_depmap.R:156:5'): plot_depmap_dependency contains correct traces ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df)) at test-plotting_depmap.R:156:5 2. │ └─base::withCallingHandlers(...) 3. ├─CRISPRball::plot_depmap_dependency(df) 4. │ ├─ggplotly(gg, tooltip = "text") %>% ... 5. │ ├─plotly::ggplotly(gg, tooltip = "text") 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 7. │ └─plotly::gg2list(...) 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density")) ── Error ('test-plotting_depmap.R:164:5'): plot_depmap_dependency assigns correct colors ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-plotting_depmap.R:164:5 2. │ └─base::withCallingHandlers(...) 3. ├─CRISPRball::plot_depmap_dependency(...) 4. │ ├─ggplotly(gg, tooltip = "text") %>% ... 5. │ ├─plotly::ggplotly(gg, tooltip = "text") 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 7. │ └─plotly::gg2list(...) 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density")) ── Error ('test-plotting_depmap.R:174:5'): plot_depmap_dependency shows dependency threshold line when depline = TRUE ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df, depline = TRUE)) at test-plotting_depmap.R:174:5 2. │ └─base::withCallingHandlers(...) 3. ├─CRISPRball::plot_depmap_dependency(df, depline = TRUE) 4. │ ├─ggplotly(gg, tooltip = "text") %>% ... 5. │ ├─plotly::ggplotly(gg, tooltip = "text") 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 7. │ └─plotly::gg2list(...) 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density")) ── Error ('test-plotting_depmap.R:181:5'): plot_depmap_dependency does not show dependency threshold line when depline = FALSE ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_dependency(df, depline = FALSE)) at test-plotting_depmap.R:181:5 2. │ └─base::withCallingHandlers(...) 3. ├─CRISPRball::plot_depmap_dependency(df, depline = FALSE) 4. │ ├─ggplotly(gg, tooltip = "text") %>% ... 5. │ ├─plotly::ggplotly(gg, tooltip = "text") 6. │ └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 7. │ └─plotly::gg2list(...) 8. └─plotly::layout(., xaxis = list(title = "Gene Effect"), yaxis = list(title = "Density")) ── Error ('test-plotting_depmap.R:197:5'): plot_depmap_expression returns a plotly object ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_expression(df.expression)) at test-plotting_depmap.R:197:5 2. │ └─base::withCallingHandlers(...) 3. └─CRISPRball::plot_depmap_expression(df.expression) 4. ├─plotly::ggplotly(gg, tooltip = "text") 5. └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 6. └─plotly::gg2list(...) ── Error ('test-plotting_depmap.R:209:5'): plot_depmap_expression assigns correct colors ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-plotting_depmap.R:209:5 2. │ └─base::withCallingHandlers(...) 3. └─CRISPRball::plot_depmap_expression(df.expression, color = "#FF0000") 4. ├─plotly::ggplotly(gg, tooltip = "text") 5. └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 6. └─plotly::gg2list(...) ── Error ('test-plotting_depmap.R:224:5'): plot_depmap_cn returns a plotly object ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_cn(df.cn)) at test-plotting_depmap.R:224:5 2. │ └─base::withCallingHandlers(...) 3. └─CRISPRball::plot_depmap_cn(df.cn) 4. ├─plotly::ggplotly(gg, tooltip = "text") 5. └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 6. └─plotly::gg2list(...) ── Error ('test-plotting_depmap.R:238:5'): plot_depmap_cn assigns correct colors ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─base::suppressWarnings(plot <- plot_depmap_cn(df.cn, color = "#FF0000")) at test-plotting_depmap.R:238:5 2. │ └─base::withCallingHandlers(...) 3. └─CRISPRball::plot_depmap_cn(df.cn, color = "#FF0000") 4. ├─plotly::ggplotly(gg, tooltip = "text") 5. └─plotly:::ggplotly.ggplot(gg, tooltip = "text") 6. └─plotly::gg2list(...) ── Error ('test-plotting_qc.R:4:5'): plot_bar returns a plotly object ────────── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "GiniIndex") at test-plotting_qc.R:4:5 2. │ ├─... %>% ... 3. │ ├─plotly::ggplotly(gg, tooltip = c("y")) 4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y")) 5. │ └─plotly::gg2list(...) 6. ├─plotly::config(...) 7. │ └─plotly:::modify_list(p$x$config, args) 8. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) 9. │ │ └─base::stopifnot(is.list(x), is.list(val)) 10. │ └─x %||% list() 11. └─plotly::layout(...) ── Error ('test-plotting_qc.R:10:5'): plot_bar handles different y parameters ── <subscriptOutOfBoundsError/error/condition> Error in `pm[[2]]`: subscript out of bounds Backtrace: ▆ 1. ├─CRISPRball::plot_bar(count.summary, x = "Label", y = "Zerocounts") at test-plotting_qc.R:10:5 2. │ ├─... %>% ... 3. │ ├─plotly::ggplotly(gg, tooltip = c("y")) 4. │ └─plotly:::ggplotly.ggplot(gg, tooltip = c("y")) 5. │ └─plotly::gg2list(...) 6. ├─plotly::config(...) 7. │ └─plotly:::modify_list(p$x$config, args) 8. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) 9. │ │ └─base::stopifnot(is.list(x), is.list(val)) 10. │ └─x %||% list() 11. └─plotly::layout(...) [ FAIL 11 | WARN 0 | SKIP 0 | PASS 120 ] Error: Test failures Execution halted
CRISPRball.Rcheck/CRISPRball-Ex.timings
name | user | system | elapsed | |
CRISPRball | 2.624 | 0.072 | 2.719 | |
build_depmap_db | 3.058 | 0.115 | 3.187 | |
gene_ingress | 0.798 | 0.035 | 0.835 | |
get_depmap_essentiality | 2.823 | 0.184 | 7.087 | |
get_depmap_plot_data | 0 | 0 | 0 | |