Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-21 12:04 -0400 (Thu, 21 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" | 4819 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4597 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4539 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1952/2318 | 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. |
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: 2025-08-21 02:50:01 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 03:00:36 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 634.6 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 (2025-06-13) * 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 ssvFeatureBinaryHeatmap 6.893 0.396 7.290 ssvFetchBam 6.373 0.016 6.327 * 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 (2025-06-13) -- "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 0 | SKIP 0 | PASS 1291 ] > > proc.time() user system elapsed 268.212 1.496 264.867
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 2.907 | 0.105 | 2.974 | |
append_ynorm | 0.076 | 0.000 | 0.046 | |
applyMovingAverage | 0.691 | 0.000 | 0.680 | |
applySpline | 0.391 | 0.003 | 0.338 | |
assemble_heatmap_cluster_bars | 0.828 | 0.017 | 0.786 | |
calc_norm_factors | 0.037 | 0.001 | 0.027 | |
centerAtMax | 0.309 | 0.015 | 0.280 | |
centerFixedSizeGRanges | 0.210 | 0.007 | 0.216 | |
centerGRangesAtMax | 0.543 | 0.002 | 0.488 | |
clusteringKmeans | 0.038 | 0.000 | 0.025 | |
clusteringKmeansNestedHclust | 0.041 | 0.000 | 0.032 | |
col2hex | 0.001 | 0.000 | 0.001 | |
collapse_gr | 0.742 | 0.004 | 0.746 | |
convert_collapsed_coord | 0.193 | 0.002 | 0.196 | |
copy_clust_info | 1.790 | 0.024 | 1.727 | |
crossCorrByRle | 0.427 | 0.011 | 0.439 | |
easyLoad_FUN | 0.053 | 0.003 | 0.057 | |
easyLoad_IDRmerged | 0.045 | 0.002 | 0.047 | |
easyLoad_bed | 0.134 | 0.002 | 0.135 | |
easyLoad_broadPeak | 0.041 | 0.000 | 0.040 | |
easyLoad_narrowPeak | 0.042 | 0.000 | 0.041 | |
easyLoad_seacr | 0.048 | 0.000 | 0.047 | |
expandCigar | 0.177 | 0.004 | 0.163 | |
findMaxPos | 0.068 | 0.001 | 0.053 | |
fragLen_calcStranded | 1.576 | 0.000 | 1.560 | |
fragLen_fromMacs2Xls | 0.002 | 0.000 | 0.002 | |
getReadLength | 0.054 | 0.001 | 0.054 | |
get_mapped_reads | 0.008 | 0.000 | 0.008 | |
ggellipse | 0.532 | 0.003 | 0.535 | |
harmonize_seqlengths | 0.102 | 0.001 | 0.103 | |
make_clustering_matrix | 0.080 | 0.001 | 0.069 | |
merge_clusters | 4.427 | 0.090 | 4.424 | |
prepare_fetch_GRanges | 0.031 | 0.000 | 0.031 | |
prepare_fetch_GRanges_names | 0.076 | 0.001 | 0.076 | |
prepare_fetch_GRanges_width | 0.028 | 0.001 | 0.029 | |
quantileGRangesWidth | 0.002 | 0.000 | 0.002 | |
reorder_clusters_hclust | 1.886 | 0.002 | 1.843 | |
reorder_clusters_manual | 1.047 | 0.025 | 0.994 | |
reorder_clusters_stepdown | 1.959 | 0.001 | 1.874 | |
reverse_clusters | 2.081 | 0.003 | 1.928 | |
safeBrew | 0.020 | 0.002 | 0.022 | |
split_cluster | 1.810 | 0.015 | 1.702 | |
ssvAnnotateSubjectGRanges | 1.070 | 0.008 | 1.079 | |
ssvConsensusIntervalSets | 0.326 | 0.005 | 0.332 | |
ssvFactorizeMembTable | 0.015 | 0.000 | 0.015 | |
ssvFeatureBars | 0.587 | 0.008 | 0.596 | |
ssvFeatureBinaryHeatmap | 6.893 | 0.396 | 7.290 | |
ssvFeatureEuler | 0.556 | 0.000 | 0.557 | |
ssvFeaturePie | 0.494 | 0.002 | 0.496 | |
ssvFeatureUpset | 2.468 | 0.001 | 2.471 | |
ssvFeatureVenn | 0.913 | 0.004 | 0.918 | |
ssvFetchBam | 6.373 | 0.016 | 6.327 | |
ssvFetchBamPE | 2.105 | 0.001 | 2.105 | |
ssvFetchBamPE.RNA | 1.617 | 0.027 | 1.576 | |
ssvFetchBigwig | 1.462 | 0.008 | 1.472 | |
ssvFetchGRanges | 0.797 | 0.002 | 0.799 | |
ssvFetchSignal | 1.507 | 0.003 | 1.511 | |
ssvMakeMembTable-methods | 0.588 | 0.001 | 0.590 | |
ssvOverlapIntervalSets | 0.254 | 0.015 | 0.268 | |
ssvSignalBandedQuantiles | 4.100 | 0.248 | 4.156 | |
ssvSignalClustering | 2.952 | 0.240 | 3.045 | |
ssvSignalHeatmap.ClusterBars | 3.557 | 0.183 | 3.562 | |
ssvSignalHeatmap | 4.340 | 0.185 | 4.154 | |
ssvSignalLineplot | 2.318 | 0.061 | 2.366 | |
ssvSignalLineplotAgg | 0.802 | 0.015 | 0.800 | |
ssvSignalScatterplot | 0.940 | 0.049 | 0.939 | |
viewGRangesWinSample_dt | 1.214 | 0.046 | 1.255 | |
viewGRangesWinSummary_dt | 1.157 | 0.003 | 1.134 | |
within_clust_sort | 1.583 | 0.041 | 1.557 | |