| Back to Build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 177/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BindingSiteFinder 2.7.1 (landing page) Mirko Brüggemann
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ||||||||
|
To the developers/maintainers of the BindingSiteFinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BindingSiteFinder.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: BindingSiteFinder |
| Version: 2.7.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.7.1.tar.gz |
| StartedAt: 2025-10-26 18:51:09 -0400 (Sun, 26 Oct 2025) |
| EndedAt: 2025-10-26 18:55:53 -0400 (Sun, 26 Oct 2025) |
| EllapsedTime: 283.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BindingSiteFinder.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.7.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.7.1’
* 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 ‘BindingSiteFinder’ 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
BSFind.Rd: GenomicRanges, CompressedGRangesList
annotateWithScore.Rd: GenomicRanges
assignToGenes.Rd: GenomicRanges, overlaps
assignToTranscriptRegions.Rd: CompressedGRangesList, overlaps
bindingSiteDefinednessPlot.Rd: ggplot
calculateBsBackground.Rd: GenomicRanges
duplicatedSitesPlot.Rd: ggplot
estimateBsWidth.Rd: GenomicRanges
estimateBsWidthPlot.Rd: ggplot
geneOverlapsPlot.Rd: ggplot
geneRegulationPlot.Rd: GenomicRanges
globalScorePlot.Rd: ggplot
makeBsSummaryPlot.Rd: ggplot
mergeCrosslinkDiagnosticsPlot.Rd: ggplot
plotBsBackgroundFilter.Rd: ggplot
plotBsMA.Rd: ggplot
plotBsVolcano.Rd: ggplot
processingStepsFlowChart.Rd: ggplot
pureClipGeneWiseFilter.Rd: GenomicRanges, overlaps
pureClipGlobalFilter.Rd: GenomicRanges
pureClipGlobalFilterPlot.Rd: ggplot
reproducibilityFilterPlot.Rd: ggplot
reproducibilitySamplesPlot.Rd: ggplot
targetGeneSpectrumPlot.Rd: ggplot
transcriptRegionOverlapsPlot.Rd: ggplot
transcriptRegionSpectrumPlot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
BSFind 8.810 0.158 10.378
quickFigure 8.676 0.132 8.822
bindingSiteDefinednessPlot 7.509 0.193 7.706
processingStepsFlowChart 7.461 0.113 7.576
calculateBsFoldChange 5.719 0.121 5.844
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck/00check.log’
for details.
BindingSiteFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BindingSiteFinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BindingSiteFinder’ ... ** this is package ‘BindingSiteFinder’ version ‘2.7.1’ ** 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 (BindingSiteFinder)
BindingSiteFinder.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
> library("BindingSiteFinder")
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
> test_check("BindingSiteFinder")
[1] "make bs"
[1] "calc ratio"
[1] "make bs"
[1] "calc ratio"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ]
>
> proc.time()
user system elapsed
76.572 1.195 77.789
BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings
| name | user | system | elapsed | |
| BSFDataSet | 0.095 | 0.004 | 0.140 | |
| BSFind | 8.810 | 0.158 | 10.378 | |
| add-BSFDataSet | 0.638 | 0.013 | 0.651 | |
| annotateWithScore | 0.407 | 0.003 | 0.414 | |
| assignToGenes | 0.625 | 0.007 | 0.635 | |
| assignToTranscriptRegions | 0.744 | 0.010 | 0.759 | |
| bindingSiteCoveragePlot | 3.771 | 0.119 | 3.903 | |
| bindingSiteDefinednessPlot | 7.509 | 0.193 | 7.706 | |
| calculateBsBackground | 1.746 | 0.033 | 1.779 | |
| calculateBsFoldChange | 5.719 | 0.121 | 5.844 | |
| calculateSignalToFlankScore | 0.452 | 0.016 | 0.468 | |
| clipCoverage | 0.513 | 0.010 | 0.522 | |
| collapseReplicates | 0.060 | 0.005 | 0.065 | |
| combineBSF | 0.929 | 0.037 | 0.967 | |
| coverageOverRanges | 0.289 | 0.015 | 0.304 | |
| duplicatedSitesPlot | 0.203 | 0.003 | 0.206 | |
| estimateBsWidth | 3.515 | 0.167 | 3.729 | |
| estimateBsWidthPlot | 2.524 | 0.037 | 2.562 | |
| exportTargetGenes | 0.019 | 0.000 | 0.020 | |
| exportToBED | 0.020 | 0.000 | 0.019 | |
| filterBsBackground | 0.983 | 0.003 | 0.986 | |
| geneOverlapsPlot | 0.765 | 0.015 | 0.780 | |
| geneRegulationPlot | 3.484 | 0.044 | 3.530 | |
| getMeta | 0.023 | 0.001 | 0.025 | |
| getName | 0.023 | 0.002 | 0.025 | |
| getRanges | 0.029 | 0.001 | 0.030 | |
| getSignal | 0.036 | 0.001 | 0.036 | |
| getSummary | 0.384 | 0.008 | 0.392 | |
| globalScorePlot | 0.469 | 0.011 | 0.481 | |
| imputeBsDifferencesForTestdata | 0.728 | 0.029 | 0.758 | |
| makeBindingSites | 0.655 | 0.023 | 0.677 | |
| makeBsSummaryPlot | 0.380 | 0.004 | 0.387 | |
| mergeCrosslinkDiagnosticsPlot | 0.469 | 0.015 | 0.490 | |
| mergeSummaryPlot | 1.087 | 0.009 | 1.096 | |
| plotBsBackgroundFilter | 1.434 | 0.025 | 1.479 | |
| plotBsMA | 4.007 | 0.049 | 4.057 | |
| plotBsVolcano | 3.678 | 0.057 | 3.735 | |
| processingStepsFlowChart | 7.461 | 0.113 | 7.576 | |
| processingStepsTable | 0.031 | 0.001 | 0.032 | |
| pureClipGeneWiseFilter | 0.117 | 0.003 | 0.119 | |
| pureClipGlobalFilter | 0.030 | 0.001 | 0.031 | |
| pureClipGlobalFilterPlot | 0.124 | 0.003 | 0.126 | |
| quickFigure | 8.676 | 0.132 | 8.822 | |
| rangeCoveragePlot | 1.764 | 0.038 | 1.804 | |
| reproducibilityCutoffPlot | 0.948 | 0.039 | 0.987 | |
| reproducibilityFilter | 0.467 | 0.005 | 0.472 | |
| reproducibilityFilterPlot | 0.664 | 0.004 | 0.668 | |
| reproducibilitySamplesPlot | 0.539 | 0.005 | 0.544 | |
| reproducibilityScatterPlot | 1.562 | 0.020 | 1.585 | |
| setMeta | 0.025 | 0.001 | 0.026 | |
| setName | 0.023 | 0.001 | 0.024 | |
| setRanges | 0.032 | 0.001 | 0.033 | |
| setSignal | 0.033 | 0.001 | 0.034 | |
| setSummary | 0.023 | 0.001 | 0.025 | |
| show | 0.023 | 0.001 | 0.024 | |
| subset-BSFDataSet | 0.027 | 0.001 | 0.028 | |
| summary | 0.030 | 0.001 | 0.031 | |
| supportRatio | 1.376 | 0.059 | 1.434 | |
| supportRatioPlot | 1.094 | 0.028 | 1.123 | |
| targetGeneSpectrumPlot | 0.708 | 0.010 | 0.719 | |
| transcriptRegionOverlapsPlot | 0.779 | 0.011 | 0.790 | |
| transcriptRegionSpectrumPlot | 0.805 | 0.009 | 0.813 | |