Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | ![]() | ||||||||
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: 1.24.0 |
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: 2024-06-24 03:49:13 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 03:59:05 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 592.3 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 4.4.0 (2024-04-24) * 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 7.629 0.367 7.997 ssvFetchBam 5.735 0.040 5.726 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 240.921 2.585 238.993
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 2.881 | 0.216 | 3.057 | |
append_ynorm | 0.058 | 0.004 | 0.038 | |
applyMovingAverage | 0.604 | 0.056 | 0.654 | |
applySpline | 0.330 | 0.028 | 0.324 | |
assemble_heatmap_cluster_bars | 0.675 | 0.012 | 0.657 | |
calc_norm_factors | 0.018 | 0.004 | 0.013 | |
centerAtMax | 0.317 | 0.012 | 0.261 | |
centerFixedSizeGRanges | 0.126 | 0.008 | 0.134 | |
centerGRangesAtMax | 0.352 | 0.020 | 0.336 | |
clusteringKmeans | 0.030 | 0.000 | 0.016 | |
clusteringKmeansNestedHclust | 0.028 | 0.007 | 0.023 | |
col2hex | 0.001 | 0.001 | 0.002 | |
collapse_gr | 0.661 | 0.028 | 0.690 | |
convert_collapsed_coord | 0.150 | 0.000 | 0.151 | |
copy_clust_info | 1.443 | 0.024 | 1.384 | |
crossCorrByRle | 0.287 | 0.012 | 0.300 | |
easyLoad_FUN | 0.049 | 0.000 | 0.049 | |
easyLoad_IDRmerged | 0.04 | 0.00 | 0.04 | |
easyLoad_bed | 0.112 | 0.004 | 0.115 | |
easyLoad_broadPeak | 0.034 | 0.000 | 0.034 | |
easyLoad_narrowPeak | 0.034 | 0.000 | 0.034 | |
easyLoad_seacr | 0.037 | 0.000 | 0.037 | |
expandCigar | 0.165 | 0.000 | 0.145 | |
findMaxPos | 0.025 | 0.000 | 0.017 | |
fragLen_calcStranded | 1.489 | 0.004 | 1.483 | |
fragLen_fromMacs2Xls | 0.002 | 0.000 | 0.003 | |
getReadLength | 0.045 | 0.004 | 0.049 | |
get_mapped_reads | 0.009 | 0.000 | 0.008 | |
ggellipse | 0.480 | 0.008 | 0.487 | |
harmonize_seqlengths | 0.080 | 0.016 | 0.097 | |
make_clustering_matrix | 0.050 | 0.003 | 0.040 | |
merge_clusters | 3.163 | 0.088 | 3.157 | |
prepare_fetch_GRanges | 0.031 | 0.000 | 0.031 | |
prepare_fetch_GRanges_names | 0.081 | 0.001 | 0.081 | |
prepare_fetch_GRanges_width | 0.029 | 0.000 | 0.029 | |
quantileGRangesWidth | 0.001 | 0.000 | 0.002 | |
reorder_clusters_hclust | 1.788 | 0.008 | 1.749 | |
reorder_clusters_manual | 0.913 | 0.011 | 0.885 | |
reorder_clusters_stepdown | 1.699 | 0.024 | 1.681 | |
reverse_clusters | 1.966 | 0.044 | 1.920 | |
safeBrew | 0.023 | 0.000 | 0.023 | |
split_cluster | 1.667 | 0.020 | 1.593 | |
ssvConsensusIntervalSets | 0.300 | 0.008 | 0.307 | |
ssvFactorizeMembTable | 0.011 | 0.004 | 0.015 | |
ssvFeatureBars | 0.542 | 0.016 | 0.558 | |
ssvFeatureBinaryHeatmap | 7.629 | 0.367 | 7.997 | |
ssvFeatureEuler | 0.603 | 0.008 | 0.611 | |
ssvFeaturePie | 0.539 | 0.032 | 0.571 | |
ssvFeatureUpset | 2.269 | 0.076 | 2.345 | |
ssvFeatureVenn | 0.853 | 0.012 | 0.866 | |
ssvFetchBam | 5.735 | 0.040 | 5.726 | |
ssvFetchBamPE | 1.796 | 0.016 | 1.812 | |
ssvFetchBigwig | 1.253 | 0.004 | 1.257 | |
ssvFetchGRanges | 0.662 | 0.000 | 0.662 | |
ssvFetchSignal | 1.328 | 0.020 | 1.349 | |
ssvMakeMembTable-methods | 0.435 | 0.010 | 0.446 | |
ssvOverlapIntervalSets | 0.208 | 0.000 | 0.208 | |
ssvSignalBandedQuantiles | 3.530 | 0.060 | 3.467 | |
ssvSignalClustering | 1.916 | 0.036 | 1.857 | |
ssvSignalHeatmap.ClusterBars | 3.819 | 0.080 | 3.725 | |
ssvSignalHeatmap | 3.191 | 0.008 | 2.973 | |
ssvSignalLineplot | 1.871 | 0.004 | 1.870 | |
ssvSignalLineplotAgg | 0.689 | 0.004 | 0.665 | |
ssvSignalScatterplot | 0.753 | 0.012 | 0.721 | |
viewGRangesWinSample_dt | 1.072 | 0.024 | 1.089 | |
viewGRangesWinSummary_dt | 1.044 | 0.000 | 1.011 | |
within_clust_sort | 1.492 | 0.008 | 1.419 | |