Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.24.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings seqsetvis_1.24.0.tar.gz |
StartedAt: 2024-07-22 04:59:19 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 05:09:02 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 582.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings seqsetvis_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 6.586 0.348 6.934 ssvFetchBam 5.845 0.044 5.853 * 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-3.19-bioc/R/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 1266 ] > > proc.time() user system elapsed 237.924 2.613 236.102
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 2.779 | 0.156 | 2.899 | |
append_ynorm | 0.063 | 0.008 | 0.039 | |
applyMovingAverage | 0.632 | 0.072 | 0.693 | |
applySpline | 0.354 | 0.000 | 0.294 | |
assemble_heatmap_cluster_bars | 0.672 | 0.012 | 0.651 | |
calc_norm_factors | 0.022 | 0.000 | 0.012 | |
centerAtMax | 0.327 | 0.012 | 0.267 | |
centerFixedSizeGRanges | 0.117 | 0.000 | 0.117 | |
centerGRangesAtMax | 0.375 | 0.012 | 0.318 | |
clusteringKmeans | 0.030 | 0.000 | 0.018 | |
clusteringKmeansNestedHclust | 0.040 | 0.004 | 0.022 | |
col2hex | 0.001 | 0.000 | 0.002 | |
collapse_gr | 0.601 | 0.012 | 0.613 | |
convert_collapsed_coord | 0.159 | 0.004 | 0.163 | |
copy_clust_info | 1.604 | 0.044 | 1.510 | |
crossCorrByRle | 0.317 | 0.004 | 0.322 | |
easyLoad_FUN | 0.049 | 0.000 | 0.049 | |
easyLoad_IDRmerged | 0.048 | 0.000 | 0.048 | |
easyLoad_bed | 0.132 | 0.000 | 0.132 | |
easyLoad_broadPeak | 0.035 | 0.000 | 0.035 | |
easyLoad_narrowPeak | 0.037 | 0.000 | 0.037 | |
easyLoad_seacr | 0.039 | 0.000 | 0.040 | |
expandCigar | 0.157 | 0.008 | 0.146 | |
findMaxPos | 0.022 | 0.004 | 0.016 | |
fragLen_calcStranded | 1.535 | 0.036 | 1.563 | |
fragLen_fromMacs2Xls | 0.003 | 0.000 | 0.002 | |
getReadLength | 0.049 | 0.004 | 0.053 | |
get_mapped_reads | 0.005 | 0.004 | 0.009 | |
ggellipse | 0.503 | 0.012 | 0.514 | |
harmonize_seqlengths | 0.098 | 0.004 | 0.103 | |
make_clustering_matrix | 0.049 | 0.001 | 0.041 | |
merge_clusters | 3.023 | 0.040 | 2.971 | |
prepare_fetch_GRanges | 0.027 | 0.000 | 0.028 | |
prepare_fetch_GRanges_names | 0.075 | 0.000 | 0.075 | |
prepare_fetch_GRanges_width | 0.023 | 0.004 | 0.026 | |
quantileGRangesWidth | 0.001 | 0.000 | 0.001 | |
reorder_clusters_hclust | 1.718 | 0.004 | 1.675 | |
reorder_clusters_manual | 0.997 | 0.012 | 0.969 | |
reorder_clusters_stepdown | 1.789 | 0.004 | 1.746 | |
reverse_clusters | 1.907 | 0.033 | 1.851 | |
safeBrew | 0.024 | 0.000 | 0.024 | |
split_cluster | 2.541 | 0.060 | 2.513 | |
ssvConsensusIntervalSets | 0.302 | 0.008 | 0.310 | |
ssvFactorizeMembTable | 0.010 | 0.004 | 0.014 | |
ssvFeatureBars | 0.514 | 0.000 | 0.513 | |
ssvFeatureBinaryHeatmap | 6.586 | 0.348 | 6.934 | |
ssvFeatureEuler | 0.470 | 0.004 | 0.474 | |
ssvFeaturePie | 0.553 | 0.012 | 0.564 | |
ssvFeatureUpset | 2.179 | 0.008 | 2.187 | |
ssvFeatureVenn | 0.822 | 0.000 | 0.822 | |
ssvFetchBam | 5.845 | 0.044 | 5.853 | |
ssvFetchBamPE | 1.773 | 0.008 | 1.781 | |
ssvFetchBigwig | 1.232 | 0.032 | 1.265 | |
ssvFetchGRanges | 0.684 | 0.000 | 0.684 | |
ssvFetchSignal | 1.346 | 0.004 | 1.350 | |
ssvMakeMembTable-methods | 0.483 | 0.000 | 0.483 | |
ssvOverlapIntervalSets | 0.230 | 0.004 | 0.233 | |
ssvSignalBandedQuantiles | 3.473 | 0.040 | 3.401 | |
ssvSignalClustering | 1.997 | 0.012 | 1.919 | |
ssvSignalHeatmap.ClusterBars | 3.089 | 0.024 | 2.997 | |
ssvSignalHeatmap | 3.419 | 0.024 | 3.177 | |
ssvSignalLineplot | 1.974 | 0.004 | 1.973 | |
ssvSignalLineplotAgg | 0.717 | 0.000 | 0.691 | |
ssvSignalScatterplot | 0.772 | 0.008 | 0.722 | |
viewGRangesWinSample_dt | 1.099 | 0.003 | 1.098 | |
viewGRangesWinSummary_dt | 1.076 | 0.000 | 1.046 | |
within_clust_sort | 1.334 | 0.004 | 1.238 | |