Jack Fu
| Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ballgown |
| git_branch: devel |
| git_last_commit: b6d07d9 |
| git_last_commit_date: 2025-07-22 22:14:37 -0400 (Tue, 22 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-23 12:04 -0400 (Sat, 23 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 125/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ballgown 2.41.1 (landing page) Jack Fu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 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 ballgown package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ballgown.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: ballgown |
| Version: 2.41.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ballgown_2.41.1.tar.gz |
| StartedAt: 2025-08-22 19:09:21 -0400 (Fri, 22 Aug 2025) |
| EndedAt: 2025-08-22 19:16:25 -0400 (Fri, 22 Aug 2025) |
| EllapsedTime: 423.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ballgown.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ballgown_2.41.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ballgown.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.41.1’
* 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 ‘ballgown’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
Version 1.99.6 released in Bioconductor 3.1 as Version 2.1.0.
Cannot process chunk/lines:
Version 0.99.1 was released on Bioconductor on 28 July 2014
* 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 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 ... NOTE
.readExon: no visible global function definition for ‘read.table’
.readIntron: no visible global function definition for ‘read.table’
.readTranscript: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘lines’
assessSim: no visible global function definition for ‘legend’
ballgown: no visible global function definition for ‘read.table’
ballgownrsem: no visible global function definition for ‘read.table’
ballgownrsem : <anonymous>: no visible global function definition for
‘read.table’
checkAssembledTx: no visible global function definition for ‘par’
checkAssembledTx: no visible global function definition for ‘polygon’
checkAssembledTx: no visible global function definition for ‘lines’
checkAssembledTx: no visible global function definition for ‘abline’
checkAssembledTx: no visible global function definition for ‘title’
checkAssembledTx: no visible global function definition for ‘axis’
closestColor: no visible global function definition for ‘heat.colors’
clusterTranscripts: no visible global function definition for ‘cutree’
clusterTranscripts: no visible global function definition for ‘hclust’
clusterTranscripts: no visible global function definition for ‘as.dist’
clusterTranscripts: no visible global function definition for ‘kmeans’
gffRead: no visible global function definition for ‘read.table’
plotMeans: no visible global function definition for ‘par’
plotMeans: no visible global function definition for ‘polygon’
plotMeans: no visible global function definition for ‘lines’
plotMeans: no visible global function definition for ‘heat.colors’
plotMeans: no visible global function definition for ‘text’
plotMeans: no visible global function definition for ‘axis’
plotTranscripts: no visible global function definition for ‘par’
plotTranscripts: no visible global function definition for ‘title’
plotTranscripts: no visible global function definition for ‘polygon’
plotTranscripts: no visible global function definition for ‘lines’
plotTranscripts: no visible global function definition for
‘heat.colors’
plotTranscripts: no visible global function definition for ‘text’
plotTranscripts: no visible global function definition for ‘axis’
stattest: no visible global function definition for ‘model.matrix’
stattest: no visible global function definition for ‘p.adjust’
writeFiles: no visible global function definition for ‘write.table’
subset,ballgown: no visible binding for global variable ‘i_id’
subset,ballgown: no visible binding for global variable ‘e_id’
subset,ballgown: no visible binding for global variable ‘t_id’
Undefined global functions or variables:
abline as.dist axis cutree e_id hclust heat.colors i_id kmeans legend
lines model.matrix p.adjust par polygon read.table t_id text title
write.table
Consider adding
importFrom("grDevices", "heat.colors")
importFrom("graphics", "abline", "axis", "legend", "lines", "par",
"polygon", "text", "title")
importFrom("stats", "as.dist", "cutree", "hclust", "kmeans",
"model.matrix", "p.adjust")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_assembly 24.38 0.231 24.738
contains 11.89 0.106 12.069
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* 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 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ballgown.Rcheck/00check.log’
for details.
ballgown.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ballgown ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ballgown’ ... ** this is package ‘ballgown’ version ‘2.41.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘structure’ in package ‘ballgown’ ** 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 (ballgown)
ballgown.Rcheck/tests/test-all.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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)
> test_check('ballgown')
Loading required package: ballgown
Attaching package: 'ballgown'
The following object is masked from 'package:base':
structure
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
>
> proc.time()
user system elapsed
109.925 1.487 112.058
ballgown.Rcheck/ballgown-Ex.timings
| name | user | system | elapsed | |
| annotate_assembly | 24.380 | 0.231 | 24.738 | |
| ballgown-class | 0.051 | 0.003 | 0.053 | |
| ballgown-constructor | 0.193 | 0.026 | 0.227 | |
| ballgownrsem | 1.547 | 0.024 | 1.585 | |
| bg | 0.024 | 0.002 | 0.027 | |
| checkAssembledTx | 0 | 0 | 0 | |
| clusterTranscripts | 0.331 | 0.004 | 0.342 | |
| collapseTranscripts | 0.389 | 0.005 | 0.398 | |
| contains | 11.890 | 0.106 | 12.069 | |
| dirs | 0.024 | 0.002 | 0.027 | |
| eexpr | 0.025 | 0.002 | 0.027 | |
| expr-replace | 0.025 | 0.002 | 0.027 | |
| expr | 0.021 | 0.002 | 0.023 | |
| exprfilter | 0.051 | 0.002 | 0.053 | |
| geneIDs | 0.022 | 0.003 | 0.025 | |
| geneNames | 0.327 | 0.007 | 0.336 | |
| getAttributeField | 0.770 | 0.007 | 0.781 | |
| getGenes | 0.287 | 0.005 | 0.293 | |
| gexpr | 0.119 | 0.003 | 0.122 | |
| gffRead | 0.115 | 0.002 | 0.118 | |
| gffReadGR | 1.195 | 0.009 | 1.209 | |
| iexpr | 0.024 | 0.001 | 0.025 | |
| indexes-replace | 0.022 | 0.001 | 0.024 | |
| indexes | 0.023 | 0.002 | 0.025 | |
| last | 0.001 | 0.000 | 0.001 | |
| mergedDate | 0.021 | 0.001 | 0.022 | |
| pData-replace | 0.022 | 0.002 | 0.025 | |
| pData | 0.020 | 0.001 | 0.021 | |
| pctOverlap | 0.265 | 0.004 | 0.271 | |
| plotLatentTranscripts | 0 | 0 | 0 | |
| plotMeans | 0 | 0 | 0 | |
| plotTranscripts | 0.000 | 0.000 | 0.001 | |
| sampleNames | 0.022 | 0.001 | 0.024 | |
| seqnames | 0.023 | 0.001 | 0.024 | |
| stattest | 0.067 | 0.003 | 0.070 | |
| structure | 0.035 | 0.002 | 0.036 | |
| subset | 0.153 | 0.003 | 0.156 | |
| tGene | 0.027 | 0.002 | 0.029 | |
| texpr | 0.022 | 0.002 | 0.024 | |
| transcriptIDs | 0.022 | 0.003 | 0.024 | |
| transcriptNames | 0.024 | 0.004 | 0.030 | |
| writeFiles | 0 | 0 | 0 | |