Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:41:06 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 1948/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.24.0 (landing page) Joseph R Boyd
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.24.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings seqsetvis_1.24.0.tar.gz |
StartedAt: 2024-05-04 11:56:51 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 12:09:29 -0000 (Sat, 04 May 2024) |
EllapsedTime: 758.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings seqsetvis_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.24.0’ * 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 LazyData ... 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 9.458 0.172 9.646 ssvFetchBam 8.818 0.047 8.884 ssvSignalBandedQuantiles 5.160 0.020 5.178 * 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-beta-2024-04-15_r86425/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘seqsetvis’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 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 0 | SKIP 0 | PASS 1266 ] > > proc.time() user system elapsed 349.376 2.471 352.198
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 3.953 | 0.088 | 4.043 | |
append_ynorm | 0.051 | 0.000 | 0.048 | |
applyMovingAverage | 0.997 | 0.004 | 1.002 | |
applySpline | 0.494 | 0.000 | 0.495 | |
assemble_heatmap_cluster_bars | 1.044 | 0.008 | 1.051 | |
calc_norm_factors | 0.015 | 0.003 | 0.018 | |
centerAtMax | 0.379 | 0.001 | 0.375 | |
centerFixedSizeGRanges | 0.195 | 0.000 | 0.196 | |
centerGRangesAtMax | 0.508 | 0.020 | 0.523 | |
clusteringKmeans | 0.026 | 0.000 | 0.022 | |
clusteringKmeansNestedHclust | 0.033 | 0.000 | 0.031 | |
col2hex | 0.002 | 0.000 | 0.001 | |
collapse_gr | 1.003 | 0.000 | 1.005 | |
convert_collapsed_coord | 0.263 | 0.008 | 0.271 | |
copy_clust_info | 2.294 | 0.024 | 2.316 | |
crossCorrByRle | 0.474 | 0.012 | 0.489 | |
easyLoad_FUN | 0.068 | 0.004 | 0.073 | |
easyLoad_IDRmerged | 0.059 | 0.000 | 0.061 | |
easyLoad_bed | 0.180 | 0.000 | 0.181 | |
easyLoad_broadPeak | 0.051 | 0.000 | 0.053 | |
easyLoad_narrowPeak | 0.054 | 0.000 | 0.055 | |
easyLoad_seacr | 0.059 | 0.000 | 0.060 | |
expandCigar | 0.218 | 0.004 | 0.221 | |
findMaxPos | 0.021 | 0.000 | 0.020 | |
fragLen_calcStranded | 2.535 | 0.024 | 2.563 | |
fragLen_fromMacs2Xls | 0.003 | 0.000 | 0.004 | |
getReadLength | 0.073 | 0.000 | 0.073 | |
get_mapped_reads | 0.011 | 0.000 | 0.011 | |
ggellipse | 0.789 | 0.004 | 0.794 | |
harmonize_seqlengths | 0.147 | 0.000 | 0.147 | |
make_clustering_matrix | 0.063 | 0.000 | 0.059 | |
merge_clusters | 4.860 | 0.035 | 4.893 | |
prepare_fetch_GRanges | 0.041 | 0.000 | 0.041 | |
prepare_fetch_GRanges_names | 0.116 | 0.000 | 0.116 | |
prepare_fetch_GRanges_width | 0.041 | 0.000 | 0.041 | |
quantileGRangesWidth | 0.002 | 0.001 | 0.002 | |
reorder_clusters_hclust | 2.853 | 0.020 | 2.871 | |
reorder_clusters_manual | 1.417 | 0.004 | 1.417 | |
reorder_clusters_stepdown | 2.844 | 0.032 | 2.875 | |
reverse_clusters | 3.065 | 0.040 | 3.095 | |
safeBrew | 0.029 | 0.004 | 0.032 | |
split_cluster | 2.672 | 0.011 | 2.670 | |
ssvConsensusIntervalSets | 0.402 | 0.016 | 0.419 | |
ssvFactorizeMembTable | 0.017 | 0.000 | 0.017 | |
ssvFeatureBars | 0.730 | 0.020 | 0.752 | |
ssvFeatureBinaryHeatmap | 9.458 | 0.172 | 9.646 | |
ssvFeatureEuler | 0.678 | 0.012 | 0.692 | |
ssvFeaturePie | 1.707 | 0.036 | 1.746 | |
ssvFeatureUpset | 3.277 | 0.056 | 3.340 | |
ssvFeatureVenn | 1.205 | 0.000 | 1.207 | |
ssvFetchBam | 8.818 | 0.047 | 8.884 | |
ssvFetchBamPE | 2.692 | 0.000 | 2.701 | |
ssvFetchBigwig | 1.869 | 0.032 | 1.911 | |
ssvFetchGRanges | 0.991 | 0.000 | 0.993 | |
ssvFetchSignal | 2.093 | 0.004 | 2.101 | |
ssvMakeMembTable-methods | 0.686 | 0.008 | 0.695 | |
ssvOverlapIntervalSets | 0.318 | 0.000 | 0.319 | |
ssvSignalBandedQuantiles | 5.160 | 0.020 | 5.178 | |
ssvSignalClustering | 2.798 | 0.039 | 2.832 | |
ssvSignalHeatmap.ClusterBars | 4.200 | 0.000 | 4.181 | |
ssvSignalHeatmap | 4.876 | 0.024 | 4.872 | |
ssvSignalLineplot | 3.016 | 0.011 | 3.034 | |
ssvSignalLineplotAgg | 1.060 | 0.008 | 1.071 | |
ssvSignalScatterplot | 1.133 | 0.000 | 1.133 | |
viewGRangesWinSample_dt | 1.735 | 0.004 | 1.742 | |
viewGRangesWinSummary_dt | 1.646 | 0.008 | 1.656 | |
within_clust_sort | 2.065 | 0.008 | 2.068 | |