Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1894/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.25.0 (landing page) Joseph R Boyd
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.25.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.25.0.tar.gz |
StartedAt: 2024-06-10 09:37:13 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 09:52:02 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 889.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings seqsetvis_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'seqsetvis/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'seqsetvis' version '1.25.0' * 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 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 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 7.81 0.39 8.63 ssvSignalHeatmap 5.03 0.10 6.53 merge_clusters 4.47 0.05 5.71 ssvSignalHeatmap.ClusterBars 4.39 0.04 5.93 ssvConsensusIntervalSets 0.44 1.41 5.98 harmonize_seqlengths 0.17 1.53 6.00 * 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 37 | PASS 800 ] ══ Skipped tests (37) ══════════════════════════════════════════════════════════ • On Windows (37): 'test_anchor.R:203:5', 'test_anchor.R:258:5', 'test_fetchBam.R:98:5', 'test_fetchBam.R:142:5', 'test_fetchBam.R:170:5', 'test_fetchBam.R:201:5', 'test_fetchBw.R:17:5', 'test_fetchBw.R:32:5', 'test_fetchBw.R:46:5', 'test_fetchBw.R:63:5', 'test_fetchBw.R:73:5', 'test_fetchBw.R:86:5', 'test_fetchBw.R:97:5', 'test_fetchBw.R:108:5', 'test_fetchBw.R:120:5', 'test_fetchBw.R:143:5', 'test_fetchBw.R:153:5', 'test_fetchBw.R:165:5', 'test_fetchBw.R:175:5', 'test_fetchBw.R:190:5', 'test_fetchBw.R:205:5', 'test_fetchBw.R:220:5', 'test_fetchBw_dt.R:15:5', 'test_fetchBw_dt.R:31:5', 'test_fetchBw_dt.R:46:5', 'test_fetchBw_dt.R:64:5', 'test_fetchBw_dt.R:74:5', 'test_fetchBw_dt.R:87:5', 'test_fetchBw_dt.R:98:5', 'test_fetchBw_dt.R:109:5', 'test_fetchBw_dt.R:121:5', 'test_fetchBw_dt.R:133:5', 'test_fetch_parallel.R:16:5', 'test_fetch_parallel.R:44:5', 'test_force_skip.R:33:5', 'test_viewGrangesWin_sample_vs_summary.R:115:5', 'test_viewGrangesWin_sample_vs_summary.R:136:5' [ FAIL 0 | WARN 0 | SKIP 37 | PASS 800 ] > > proc.time() user system elapsed 193.29 18.89 212.68
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 3.76 | 0.22 | 4.14 | |
append_ynorm | 0.06 | 0.00 | 0.08 | |
applyMovingAverage | 0.97 | 0.01 | 0.98 | |
applySpline | 0.39 | 0.06 | 0.54 | |
assemble_heatmap_cluster_bars | 0.97 | 0.04 | 1.09 | |
calc_norm_factors | 0.00 | 0.00 | 0.01 | |
centerAtMax | 0.33 | 0.02 | 0.45 | |
centerFixedSizeGRanges | 0.19 | 1.45 | 2.30 | |
centerGRangesAtMax | 0.36 | 0.00 | 0.37 | |
clusteringKmeans | 0.03 | 0.00 | 0.03 | |
clusteringKmeansNestedHclust | 0.01 | 0.00 | 0.02 | |
col2hex | 0 | 0 | 0 | |
collapse_gr | 0.88 | 1.53 | 3.24 | |
convert_collapsed_coord | 0.20 | 1.36 | 2.28 | |
copy_clust_info | 1.78 | 0.00 | 1.78 | |
crossCorrByRle | 0.3 | 0.0 | 0.3 | |
easyLoad_FUN | 0.06 | 0.00 | 0.06 | |
easyLoad_IDRmerged | 0.05 | 0.00 | 0.05 | |
easyLoad_bed | 0.12 | 0.00 | 0.12 | |
easyLoad_broadPeak | 0.05 | 0.00 | 0.05 | |
easyLoad_narrowPeak | 0.03 | 0.00 | 0.03 | |
easyLoad_seacr | 0.03 | 0.00 | 0.05 | |
expandCigar | 0.13 | 0.00 | 0.12 | |
findMaxPos | 0.01 | 0.00 | 0.02 | |
fragLen_calcStranded | 1.39 | 0.03 | 1.42 | |
fragLen_fromMacs2Xls | 0.00 | 0.00 | 0.02 | |
getReadLength | 0.05 | 0.00 | 0.04 | |
get_mapped_reads | 0.02 | 0.00 | 0.02 | |
ggellipse | 0.53 | 0.00 | 0.53 | |
harmonize_seqlengths | 0.17 | 1.53 | 6.00 | |
make_clustering_matrix | 0.08 | 0.00 | 0.43 | |
merge_clusters | 4.47 | 0.05 | 5.71 | |
prepare_fetch_GRanges | 0.01 | 0.00 | 0.01 | |
prepare_fetch_GRanges_names | 0.11 | 0.00 | 0.11 | |
prepare_fetch_GRanges_width | 0.03 | 0.00 | 0.03 | |
quantileGRangesWidth | 0 | 0 | 0 | |
reorder_clusters_hclust | 2.14 | 0.00 | 2.18 | |
reorder_clusters_manual | 1.27 | 0.00 | 1.29 | |
reorder_clusters_stepdown | 2.46 | 0.00 | 2.64 | |
reverse_clusters | 2.99 | 0.03 | 3.02 | |
safeBrew | 0.01 | 0.02 | 0.03 | |
split_cluster | 1.60 | 0.09 | 1.70 | |
ssvConsensusIntervalSets | 0.44 | 1.41 | 5.98 | |
ssvFactorizeMembTable | 0.02 | 0.00 | 0.01 | |
ssvFeatureBars | 0.72 | 0.01 | 0.76 | |
ssvFeatureBinaryHeatmap | 7.81 | 0.39 | 8.63 | |
ssvFeatureEuler | 0.73 | 0.00 | 0.75 | |
ssvFeaturePie | 0.85 | 0.00 | 0.86 | |
ssvFeatureUpset | 3.42 | 0.07 | 3.53 | |
ssvFeatureVenn | 1.14 | 0.04 | 1.22 | |
ssvFetchBam | 0 | 0 | 0 | |
ssvFetchBamPE | 0 | 0 | 0 | |
ssvFetchBigwig | 0 | 0 | 0 | |
ssvFetchGRanges | 1.04 | 0.02 | 1.07 | |
ssvFetchSignal | 2.07 | 1.62 | 3.88 | |
ssvMakeMembTable-methods | 0.67 | 1.43 | 2.97 | |
ssvOverlapIntervalSets | 0.41 | 1.28 | 3.74 | |
ssvSignalBandedQuantiles | 3.92 | 0.04 | 3.97 | |
ssvSignalClustering | 2.50 | 0.07 | 2.86 | |
ssvSignalHeatmap.ClusterBars | 4.39 | 0.04 | 5.93 | |
ssvSignalHeatmap | 5.03 | 0.10 | 6.53 | |
ssvSignalLineplot | 2.89 | 0.04 | 2.98 | |
ssvSignalLineplotAgg | 1.03 | 0.04 | 1.06 | |
ssvSignalScatterplot | 1.17 | 0.04 | 1.27 | |
viewGRangesWinSample_dt | 1.35 | 0.00 | 1.47 | |
viewGRangesWinSummary_dt | 1.34 | 0.00 | 1.44 | |
within_clust_sort | 2.03 | 0.02 | 2.17 | |