Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-16 12:04 -0400 (Thu, 16 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" | 4867 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4655 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4600 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 12.7.6 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 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings seqsetvis_1.29.1.tar.gz |
StartedAt: 2025-10-16 04:54:04 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 05:07:34 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 809.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings seqsetvis_1.29.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.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 ‘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 ssvFetchBamPE.RNA 16.938 0.069 2.844 ssvSignalHeatmap 12.816 0.302 6.637 ssvSignalHeatmap.ClusterBars 11.342 0.354 6.344 ssvSignalClustering 9.696 0.211 5.389 ssvSignalBandedQuantiles 7.929 0.028 4.986 merge_clusters 7.509 0.284 5.533 ssvFeatureBinaryHeatmap 7.044 0.496 7.653 ssvFetchBam 7.369 0.089 7.425 split_cluster 5.737 0.208 3.390 add_cluster_annotation 5.716 0.191 4.945 applySpline 5.704 0.038 1.031 reorder_clusters_stepdown 4.889 0.390 4.383 * 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: OK
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 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. > > ## 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 412.995 5.331 336.297
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 5.716 | 0.191 | 4.945 | |
append_ynorm | 0.128 | 0.000 | 0.055 | |
applyMovingAverage | 1.941 | 0.006 | 1.215 | |
applySpline | 5.704 | 0.038 | 1.031 | |
assemble_heatmap_cluster_bars | 2.506 | 0.020 | 1.560 | |
calc_norm_factors | 0.259 | 0.001 | 0.098 | |
centerAtMax | 1.891 | 0.012 | 0.511 | |
centerFixedSizeGRanges | 0.222 | 0.004 | 0.226 | |
centerGRangesAtMax | 2.665 | 0.057 | 0.922 | |
clusteringKmeans | 0.139 | 0.002 | 0.052 | |
clusteringKmeansNestedHclust | 0.100 | 0.004 | 0.057 | |
col2hex | 0.002 | 0.000 | 0.002 | |
collapse_gr | 0.915 | 0.022 | 0.938 | |
convert_collapsed_coord | 0.374 | 0.006 | 0.379 | |
copy_clust_info | 3.727 | 0.156 | 2.779 | |
crossCorrByRle | 0.568 | 0.011 | 0.671 | |
easyLoad_FUN | 0.072 | 0.000 | 0.080 | |
easyLoad_IDRmerged | 0.063 | 0.001 | 0.077 | |
easyLoad_bed | 0.208 | 0.000 | 0.208 | |
easyLoad_broadPeak | 0.056 | 0.000 | 0.060 | |
easyLoad_narrowPeak | 0.046 | 0.000 | 0.056 | |
easyLoad_seacr | 0.044 | 0.000 | 0.044 | |
expandCigar | 0.186 | 0.001 | 0.169 | |
findMaxPos | 0.071 | 0.001 | 0.039 | |
fragLen_calcStranded | 2.740 | 0.007 | 1.963 | |
fragLen_fromMacs2Xls | 0.003 | 0.000 | 0.002 | |
getReadLength | 0.052 | 0.000 | 0.052 | |
get_mapped_reads | 0.009 | 0.000 | 0.009 | |
ggellipse | 0.998 | 0.002 | 1.017 | |
harmonize_seqlengths | 0.134 | 0.006 | 0.139 | |
make_clustering_matrix | 0.300 | 0.001 | 0.140 | |
merge_clusters | 7.509 | 0.284 | 5.533 | |
prepare_fetch_GRanges | 0.028 | 0.005 | 0.033 | |
prepare_fetch_GRanges_names | 0.078 | 0.005 | 0.083 | |
prepare_fetch_GRanges_width | 0.027 | 0.002 | 0.029 | |
quantileGRangesWidth | 0.002 | 0.000 | 0.002 | |
reorder_clusters_hclust | 3.860 | 0.151 | 3.090 | |
reorder_clusters_manual | 3.068 | 0.132 | 1.851 | |
reorder_clusters_stepdown | 4.889 | 0.390 | 4.383 | |
reverse_clusters | 3.965 | 0.218 | 3.129 | |
safeBrew | 0.026 | 0.002 | 0.028 | |
split_cluster | 5.737 | 0.208 | 3.390 | |
ssvAnnotateSubjectGRanges | 1.172 | 0.042 | 1.226 | |
ssvConsensusIntervalSets | 0.344 | 0.003 | 0.355 | |
ssvFactorizeMembTable | 0.014 | 0.001 | 0.015 | |
ssvFeatureBars | 1.001 | 0.018 | 1.022 | |
ssvFeatureBinaryHeatmap | 7.044 | 0.496 | 7.653 | |
ssvFeatureEuler | 1.014 | 0.047 | 1.076 | |
ssvFeaturePie | 0.816 | 0.024 | 0.840 | |
ssvFeatureUpset | 4.119 | 0.069 | 4.280 | |
ssvFeatureVenn | 1.885 | 0.028 | 1.914 | |
ssvFetchBam | 7.369 | 0.089 | 7.425 | |
ssvFetchBamPE | 2.526 | 0.049 | 2.663 | |
ssvFetchBamPE.RNA | 16.938 | 0.069 | 2.844 | |
ssvFetchBigwig | 2.180 | 0.006 | 2.202 | |
ssvFetchGRanges | 1.204 | 0.001 | 1.207 | |
ssvFetchSignal | 2.174 | 0.005 | 2.180 | |
ssvMakeMembTable-methods | 0.833 | 0.001 | 0.833 | |
ssvOverlapIntervalSets | 0.346 | 0.001 | 0.347 | |
ssvSignalBandedQuantiles | 7.929 | 0.028 | 4.986 | |
ssvSignalClustering | 9.696 | 0.211 | 5.389 | |
ssvSignalHeatmap.ClusterBars | 11.342 | 0.354 | 6.344 | |
ssvSignalHeatmap | 12.816 | 0.302 | 6.637 | |
ssvSignalLineplot | 3.977 | 0.147 | 4.139 | |
ssvSignalLineplotAgg | 1.214 | 0.015 | 1.157 | |
ssvSignalScatterplot | 1.351 | 0.018 | 1.325 | |
viewGRangesWinSample_dt | 1.391 | 0.015 | 1.427 | |
viewGRangesWinSummary_dt | 2.693 | 0.055 | 1.775 | |
within_clust_sort | 3.973 | 0.240 | 3.064 | |