Thomas Carroll
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/basecallQC |
| git_branch: devel |
| git_last_commit: 3b9d7e5 |
| git_last_commit_date: 2025-04-15 11:10:19 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:03 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 136/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basecallQC 1.33.0 (landing page) Thomas Carroll
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the basecallQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basecallQC.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. |
| Package: basecallQC |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings basecallQC_1.33.0.tar.gz |
| StartedAt: 2025-10-22 21:16:48 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 21:24:11 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 443.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basecallQC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings basecallQC_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.33.0’
* 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 ‘basecallQC’ 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 ... NOTE
checkRd: (-1) BCL2FastQparams.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:38-41: Lost braces in \itemize; meant \describe ?
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
reportBCL 7.537 0.150 7.700
passFilterTileplot 5.421 0.161 5.582
baseCallMetrics 4.852 0.189 5.042
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck/00check.log’
for details.
basecallQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL basecallQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘basecallQC’ ... ** this is package ‘basecallQC’ version ‘1.33.0’ ** using staged installation ** R ** 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 (basecallQC)
basecallQC.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
>
> test_check("basecallQC")
[ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ]
[ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ]
>
> proc.time()
user system elapsed
23.215 1.053 24.258
basecallQC.Rcheck/basecallQC-Ex.timings
| name | user | system | elapsed | |
| BCL2FastQparams | 0.228 | 0.023 | 0.250 | |
| baseCallMetrics | 4.852 | 0.189 | 5.042 | |
| basecallQC | 4.223 | 0.041 | 4.264 | |
| createBCLcommand | 0.239 | 0.004 | 0.242 | |
| createBasemasks | 0.230 | 0.002 | 0.232 | |
| demultiplexMetrics | 0.048 | 0.002 | 0.051 | |
| demuxBarplot | 4.513 | 0.056 | 4.573 | |
| demuxBoxplot | 4.345 | 0.078 | 4.423 | |
| indexlengths | 0.023 | 0.000 | 0.023 | |
| interOpsReport | 0.018 | 0.000 | 0.019 | |
| makeFQTable | 4.228 | 0.058 | 4.286 | |
| passFilterBar | 4.238 | 0.010 | 4.248 | |
| passFilterBoxplot | 4.370 | 0.023 | 4.393 | |
| passFilterTileplot | 5.421 | 0.161 | 5.582 | |
| readlengths | 0.022 | 0.001 | 0.023 | |
| reportBCL | 7.537 | 0.150 | 7.700 | |
| summaryConvStatsTable | 4.224 | 0.073 | 4.297 | |
| summaryDemuxTable | 4.164 | 0.021 | 4.185 | |
| validateBCLSheet | 0.060 | 0.000 | 0.062 | |