| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1985/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqsetvis 1.29.1 (landing page) Joseph R Boyd
| 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 | NA | ||||||||||
|
To the developers/maintainers of the seqsetvis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqsetvis.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: seqsetvis |
| Version: 1.29.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.29.1.tar.gz |
| StartedAt: 2025-10-24 00:09:24 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 00:20:51 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 687.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqsetvis.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.29.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.29.1’
* 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 ‘seqsetvis’ 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 ... 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
ssvFeatureBinaryHeatmap 7.938 0.688 8.696
ssvFetchBam 6.873 0.340 7.276
ssvSignalHeatmap 6.310 0.157 6.519
ssvSignalHeatmap.ClusterBars 5.160 0.060 5.269
ssvSignalBandedQuantiles 4.902 0.070 5.038
* 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: OK
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘seqsetvis’ ... ** this is package ‘seqsetvis’ version ‘1.29.1’ ** 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 (seqsetvis)
seqsetvis.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: 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. > > ## load dependencies > library(testthat) > library(seqsetvis) Loading required package: ggplot2 > library(data.table) > > ## test package > test_check(package = "seqsetvis") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ] > > proc.time() user system elapsed 302.968 6.469 311.270
seqsetvis.Rcheck/seqsetvis-Ex.timings
| name | user | system | elapsed | |
| add_cluster_annotation | 3.833 | 0.124 | 3.993 | |
| append_ynorm | 0.061 | 0.006 | 0.068 | |
| applyMovingAverage | 1.125 | 0.016 | 1.152 | |
| applySpline | 0.558 | 0.012 | 0.575 | |
| assemble_heatmap_cluster_bars | 1.086 | 0.013 | 1.109 | |
| calc_norm_factors | 0.029 | 0.003 | 0.033 | |
| centerAtMax | 0.281 | 0.008 | 0.291 | |
| centerFixedSizeGRanges | 0.201 | 0.012 | 0.214 | |
| centerGRangesAtMax | 0.602 | 0.015 | 0.621 | |
| clusteringKmeans | 0.032 | 0.005 | 0.038 | |
| clusteringKmeansNestedHclust | 0.034 | 0.006 | 0.042 | |
| col2hex | 0.001 | 0.000 | 0.001 | |
| collapse_gr | 0.811 | 0.016 | 0.831 | |
| convert_collapsed_coord | 0.255 | 0.011 | 0.268 | |
| copy_clust_info | 2.128 | 0.026 | 2.170 | |
| crossCorrByRle | 0.516 | 0.014 | 0.536 | |
| easyLoad_FUN | 0.062 | 0.002 | 0.064 | |
| easyLoad_IDRmerged | 0.044 | 0.002 | 0.046 | |
| easyLoad_bed | 0.134 | 0.002 | 0.136 | |
| easyLoad_broadPeak | 0.058 | 0.002 | 0.060 | |
| easyLoad_narrowPeak | 0.047 | 0.002 | 0.049 | |
| easyLoad_seacr | 0.056 | 0.002 | 0.058 | |
| expandCigar | 0.177 | 0.018 | 0.195 | |
| findMaxPos | 0.037 | 0.009 | 0.046 | |
| fragLen_calcStranded | 1.871 | 0.037 | 1.922 | |
| fragLen_fromMacs2Xls | 0.002 | 0.001 | 0.004 | |
| getReadLength | 0.064 | 0.008 | 0.074 | |
| get_mapped_reads | 0.009 | 0.001 | 0.010 | |
| ggellipse | 0.970 | 0.010 | 0.987 | |
| harmonize_seqlengths | 0.157 | 0.011 | 0.169 | |
| make_clustering_matrix | 0.077 | 0.005 | 0.082 | |
| merge_clusters | 4.758 | 0.053 | 4.839 | |
| prepare_fetch_GRanges | 0.032 | 0.002 | 0.034 | |
| prepare_fetch_GRanges_names | 0.091 | 0.003 | 0.095 | |
| prepare_fetch_GRanges_width | 0.032 | 0.002 | 0.035 | |
| quantileGRangesWidth | 0.002 | 0.001 | 0.004 | |
| reorder_clusters_hclust | 2.798 | 0.029 | 2.844 | |
| reorder_clusters_manual | 2.453 | 0.054 | 2.548 | |
| reorder_clusters_stepdown | 2.705 | 0.029 | 2.750 | |
| reverse_clusters | 3.032 | 0.033 | 3.093 | |
| safeBrew | 0.026 | 0.004 | 0.032 | |
| split_cluster | 2.520 | 0.034 | 2.586 | |
| ssvAnnotateSubjectGRanges | 1.155 | 0.032 | 1.195 | |
| ssvConsensusIntervalSets | 0.380 | 0.013 | 0.394 | |
| ssvFactorizeMembTable | 0.018 | 0.006 | 0.024 | |
| ssvFeatureBars | 1.076 | 0.009 | 1.093 | |
| ssvFeatureBinaryHeatmap | 7.938 | 0.688 | 8.696 | |
| ssvFeatureEuler | 0.934 | 0.022 | 0.966 | |
| ssvFeaturePie | 0.800 | 0.014 | 0.822 | |
| ssvFeatureUpset | 3.736 | 0.061 | 3.821 | |
| ssvFeatureVenn | 1.677 | 0.017 | 1.706 | |
| ssvFetchBam | 6.873 | 0.340 | 7.276 | |
| ssvFetchBamPE | 2.195 | 0.206 | 2.423 | |
| ssvFetchBamPE.RNA | 1.780 | 0.045 | 1.843 | |
| ssvFetchBigwig | 1.527 | 0.034 | 1.576 | |
| ssvFetchGRanges | 0.816 | 0.018 | 0.842 | |
| ssvFetchSignal | 1.877 | 0.105 | 2.013 | |
| ssvMakeMembTable-methods | 0.711 | 0.018 | 0.741 | |
| ssvOverlapIntervalSets | 0.316 | 0.015 | 0.340 | |
| ssvSignalBandedQuantiles | 4.902 | 0.070 | 5.038 | |
| ssvSignalClustering | 3.882 | 0.064 | 3.999 | |
| ssvSignalHeatmap.ClusterBars | 5.160 | 0.060 | 5.269 | |
| ssvSignalHeatmap | 6.310 | 0.157 | 6.519 | |
| ssvSignalLineplot | 3.386 | 0.039 | 3.454 | |
| ssvSignalLineplotAgg | 1.145 | 0.015 | 1.167 | |
| ssvSignalScatterplot | 1.215 | 0.017 | 1.243 | |
| viewGRangesWinSample_dt | 1.287 | 0.044 | 1.339 | |
| viewGRangesWinSummary_dt | 1.307 | 0.058 | 1.372 | |
| within_clust_sort | 1.939 | 0.033 | 1.983 | |