Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:07 -0400 (Mon, 13 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" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 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 1974/2346 | 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 12.7.1 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: seqsetvis |
Version: 1.29.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqsetvis_1.29.1.tar.gz |
StartedAt: 2025-10-10 13:32:04 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 13:50:21 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 1097.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqsetvis_1.29.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * 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 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 ... 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 ssvFetchBam 9.045 0.004 12.946 ssvSignalHeatmap 7.066 0.028 8.463 ssvFeatureBinaryHeatmap 6.890 0.108 8.517 merge_clusters 6.327 0.016 9.116 ssvSignalHeatmap.ClusterBars 6.199 0.003 7.315 ssvSignalBandedQuantiles 5.849 0.024 6.532 ssvSignalClustering 5.482 0.149 9.861 add_cluster_annotation 4.761 0.117 6.541 ssvFeatureUpset 4.786 0.008 6.018 ssvSignalLineplot 4.406 0.000 7.300 reorder_clusters_stepdown 4.346 0.056 6.849 reorder_clusters_hclust 3.601 0.020 5.776 ssvFetchBamPE 2.708 0.028 5.137 * 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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. > > ## 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 386.264 1.860 516.835
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 4.761 | 0.117 | 6.541 | |
append_ynorm | 0.084 | 0.004 | 0.088 | |
applyMovingAverage | 1.355 | 0.000 | 1.481 | |
applySpline | 0.691 | 0.016 | 1.159 | |
assemble_heatmap_cluster_bars | 1.465 | 0.004 | 2.395 | |
calc_norm_factors | 0.034 | 0.000 | 0.034 | |
centerAtMax | 0.374 | 0.012 | 0.387 | |
centerFixedSizeGRanges | 0.198 | 0.000 | 0.258 | |
centerGRangesAtMax | 0.742 | 0.001 | 0.875 | |
clusteringKmeans | 0.054 | 0.004 | 0.058 | |
clusteringKmeansNestedHclust | 0.05 | 0.00 | 0.05 | |
col2hex | 0.001 | 0.000 | 0.001 | |
collapse_gr | 0.996 | 0.007 | 1.294 | |
convert_collapsed_coord | 0.354 | 0.001 | 0.711 | |
copy_clust_info | 2.496 | 0.027 | 2.749 | |
crossCorrByRle | 0.610 | 0.005 | 1.075 | |
easyLoad_FUN | 0.069 | 0.000 | 0.142 | |
easyLoad_IDRmerged | 0.056 | 0.000 | 0.116 | |
easyLoad_bed | 0.168 | 0.004 | 0.345 | |
easyLoad_broadPeak | 0.051 | 0.000 | 0.101 | |
easyLoad_narrowPeak | 0.059 | 0.000 | 0.117 | |
easyLoad_seacr | 0.072 | 0.000 | 0.149 | |
expandCigar | 0.224 | 0.004 | 0.457 | |
findMaxPos | 0.037 | 0.005 | 0.086 | |
fragLen_calcStranded | 2.504 | 0.004 | 3.350 | |
fragLen_fromMacs2Xls | 0.000 | 0.003 | 0.007 | |
getReadLength | 0.075 | 0.001 | 0.153 | |
get_mapped_reads | 0.011 | 0.000 | 0.019 | |
ggellipse | 1.258 | 0.004 | 1.457 | |
harmonize_seqlengths | 0.153 | 0.000 | 0.183 | |
make_clustering_matrix | 0.126 | 0.000 | 0.165 | |
merge_clusters | 6.327 | 0.016 | 9.116 | |
prepare_fetch_GRanges | 0.041 | 0.000 | 0.081 | |
prepare_fetch_GRanges_names | 0.112 | 0.000 | 0.224 | |
prepare_fetch_GRanges_width | 0.037 | 0.004 | 0.085 | |
quantileGRangesWidth | 0.003 | 0.000 | 0.008 | |
reorder_clusters_hclust | 3.601 | 0.020 | 5.776 | |
reorder_clusters_manual | 1.887 | 0.000 | 2.101 | |
reorder_clusters_stepdown | 4.346 | 0.056 | 6.849 | |
reverse_clusters | 3.703 | 0.024 | 4.320 | |
safeBrew | 0.029 | 0.000 | 0.028 | |
split_cluster | 3.462 | 0.012 | 3.866 | |
ssvAnnotateSubjectGRanges | 1.361 | 0.003 | 1.577 | |
ssvConsensusIntervalSets | 0.430 | 0.016 | 0.451 | |
ssvFactorizeMembTable | 0.019 | 0.000 | 0.019 | |
ssvFeatureBars | 1.334 | 0.020 | 2.270 | |
ssvFeatureBinaryHeatmap | 6.890 | 0.108 | 8.517 | |
ssvFeatureEuler | 1.298 | 0.004 | 2.615 | |
ssvFeaturePie | 1.022 | 0.004 | 2.057 | |
ssvFeatureUpset | 4.786 | 0.008 | 6.018 | |
ssvFeatureVenn | 2.216 | 0.016 | 3.831 | |
ssvFetchBam | 9.045 | 0.004 | 12.946 | |
ssvFetchBamPE | 2.708 | 0.028 | 5.137 | |
ssvFetchBamPE.RNA | 2.179 | 0.000 | 2.545 | |
ssvFetchBigwig | 2.028 | 0.004 | 3.506 | |
ssvFetchGRanges | 1.081 | 0.000 | 1.348 | |
ssvFetchSignal | 2.174 | 0.003 | 2.411 | |
ssvMakeMembTable-methods | 0.758 | 0.032 | 1.506 | |
ssvOverlapIntervalSets | 0.347 | 0.016 | 0.480 | |
ssvSignalBandedQuantiles | 5.849 | 0.024 | 6.532 | |
ssvSignalClustering | 5.482 | 0.149 | 9.861 | |
ssvSignalHeatmap.ClusterBars | 6.199 | 0.003 | 7.315 | |
ssvSignalHeatmap | 7.066 | 0.028 | 8.463 | |
ssvSignalLineplot | 4.406 | 0.000 | 7.300 | |
ssvSignalLineplotAgg | 1.503 | 0.004 | 1.755 | |
ssvSignalScatterplot | 1.701 | 0.008 | 2.762 | |
viewGRangesWinSample_dt | 1.780 | 0.012 | 1.898 | |
viewGRangesWinSummary_dt | 1.641 | 0.012 | 1.759 | |
within_clust_sort | 2.833 | 0.000 | 2.938 | |