Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1934/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.26.0 (landing page) Joseph R Boyd
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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 | ||||||||||
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: 1.26.0 |
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_1.26.0.tar.gz |
StartedAt: 2024-11-20 12:23:58 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 12:37:01 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 783.4 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘1.26.0’ * 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 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 8.852 0.012 8.879 ssvFeatureBinaryHeatmap 7.674 0.204 7.891 ssvSignalBandedQuantiles 5.309 0.032 5.337 ssvSignalHeatmap 5.196 0.047 5.215 * 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-4.4.1/site-library’ * installing *source* package ‘seqsetvis’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 1284 ] > > proc.time() user system elapsed 368.684 3.240 372.320
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 3.914 | 0.104 | 4.019 | |
append_ynorm | 0.064 | 0.008 | 0.068 | |
applyMovingAverage | 0.961 | 0.028 | 0.990 | |
applySpline | 0.482 | 0.004 | 0.480 | |
assemble_heatmap_cluster_bars | 0.999 | 0.000 | 0.994 | |
calc_norm_factors | 0.031 | 0.000 | 0.030 | |
centerAtMax | 0.357 | 0.000 | 0.352 | |
centerFixedSizeGRanges | 0.170 | 0.008 | 0.178 | |
centerGRangesAtMax | 0.532 | 0.016 | 0.544 | |
clusteringKmeans | 0.055 | 0.008 | 0.061 | |
clusteringKmeansNestedHclust | 0.045 | 0.000 | 0.042 | |
col2hex | 0.002 | 0.000 | 0.001 | |
collapse_gr | 0.978 | 0.012 | 0.991 | |
convert_collapsed_coord | 0.273 | 0.000 | 0.273 | |
copy_clust_info | 2.373 | 0.012 | 2.382 | |
crossCorrByRle | 0.456 | 0.000 | 0.460 | |
easyLoad_FUN | 0.067 | 0.000 | 0.068 | |
easyLoad_IDRmerged | 0.062 | 0.003 | 0.066 | |
easyLoad_bed | 0.222 | 0.004 | 0.227 | |
easyLoad_broadPeak | 0.05 | 0.00 | 0.05 | |
easyLoad_narrowPeak | 0.051 | 0.000 | 0.052 | |
easyLoad_seacr | 0.057 | 0.001 | 0.057 | |
expandCigar | 0.208 | 0.004 | 0.211 | |
findMaxPos | 0.043 | 0.000 | 0.042 | |
fragLen_calcStranded | 2.466 | 0.004 | 2.476 | |
fragLen_fromMacs2Xls | 0.002 | 0.000 | 0.003 | |
getReadLength | 0.071 | 0.000 | 0.071 | |
get_mapped_reads | 0.011 | 0.000 | 0.011 | |
ggellipse | 0.732 | 0.000 | 0.734 | |
harmonize_seqlengths | 0.132 | 0.004 | 0.136 | |
make_clustering_matrix | 0.147 | 0.000 | 0.147 | |
merge_clusters | 4.709 | 0.031 | 4.736 | |
prepare_fetch_GRanges | 0.04 | 0.00 | 0.04 | |
prepare_fetch_GRanges_names | 0.117 | 0.004 | 0.120 | |
prepare_fetch_GRanges_width | 0.039 | 0.004 | 0.044 | |
quantileGRangesWidth | 0.002 | 0.002 | 0.003 | |
reorder_clusters_hclust | 2.772 | 0.045 | 2.815 | |
reorder_clusters_manual | 1.465 | 0.004 | 1.466 | |
reorder_clusters_stepdown | 2.657 | 0.024 | 2.678 | |
reverse_clusters | 3.904 | 0.116 | 4.010 | |
safeBrew | 0.026 | 0.004 | 0.031 | |
split_cluster | 2.488 | 0.048 | 2.524 | |
ssvAnnotateSubjectGRanges | 1.279 | 0.008 | 1.290 | |
ssvConsensusIntervalSets | 0.497 | 0.008 | 0.505 | |
ssvFactorizeMembTable | 0.018 | 0.000 | 0.019 | |
ssvFeatureBars | 0.742 | 0.004 | 0.747 | |
ssvFeatureBinaryHeatmap | 7.674 | 0.204 | 7.891 | |
ssvFeatureEuler | 0.757 | 0.000 | 0.759 | |
ssvFeaturePie | 0.672 | 0.004 | 0.677 | |
ssvFeatureUpset | 3.432 | 0.060 | 3.498 | |
ssvFeatureVenn | 1.270 | 0.012 | 1.285 | |
ssvFetchBam | 8.852 | 0.012 | 8.879 | |
ssvFetchBamPE | 2.581 | 0.007 | 2.597 | |
ssvFetchBamPE.RNA | 1.925 | 0.016 | 1.930 | |
ssvFetchBigwig | 1.889 | 0.000 | 1.894 | |
ssvFetchGRanges | 1.039 | 0.000 | 1.040 | |
ssvFetchSignal | 2.128 | 0.004 | 2.137 | |
ssvMakeMembTable-methods | 0.708 | 0.012 | 0.721 | |
ssvOverlapIntervalSets | 0.339 | 0.004 | 0.344 | |
ssvSignalBandedQuantiles | 5.309 | 0.032 | 5.337 | |
ssvSignalClustering | 3.722 | 0.072 | 3.774 | |
ssvSignalHeatmap.ClusterBars | 4.489 | 0.028 | 4.494 | |
ssvSignalHeatmap | 5.196 | 0.047 | 5.215 | |
ssvSignalLineplot | 2.907 | 0.012 | 2.923 | |
ssvSignalLineplotAgg | 1.033 | 0.000 | 1.033 | |
ssvSignalScatterplot | 1.132 | 0.012 | 1.141 | |
viewGRangesWinSample_dt | 1.714 | 0.000 | 1.719 | |
viewGRangesWinSummary_dt | 2.638 | 0.068 | 2.708 | |
within_clust_sort | 2.040 | 0.004 | 2.036 | |