Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-27 11:38 -0400 (Thu, 27 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" | 4691 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4405 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4354 |
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 1897/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.25.2 (landing page) Joseph R Boyd
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 1.25.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.25.2.tar.gz |
StartedAt: 2024-06-26 23:04:24 -0400 (Wed, 26 Jun 2024) |
EndedAt: 2024-06-26 23:15:45 -0400 (Wed, 26 Jun 2024) |
EllapsedTime: 680.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqsetvis_1.25.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.25.2’ * 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 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 ssvFeatureBinaryHeatmap 7.664 0.720 8.447 ssvFetchBam 7.203 0.336 7.596 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 306.233 6.783 314.962
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 3.220 | 0.089 | 3.323 | |
append_ynorm | 0.052 | 0.008 | 0.061 | |
applyMovingAverage | 0.742 | 0.063 | 0.810 | |
applySpline | 0.335 | 0.007 | 0.345 | |
assemble_heatmap_cluster_bars | 0.769 | 0.009 | 0.781 | |
calc_norm_factors | 0.026 | 0.004 | 0.030 | |
centerAtMax | 0.346 | 0.018 | 0.370 | |
centerFixedSizeGRanges | 0.183 | 0.010 | 0.195 | |
centerGRangesAtMax | 0.442 | 0.012 | 0.455 | |
clusteringKmeans | 0.034 | 0.005 | 0.040 | |
clusteringKmeansNestedHclust | 0.040 | 0.004 | 0.045 | |
col2hex | 0.001 | 0.000 | 0.001 | |
collapse_gr | 0.910 | 0.017 | 0.934 | |
convert_collapsed_coord | 0.270 | 0.012 | 0.284 | |
copy_clust_info | 1.886 | 0.022 | 1.922 | |
crossCorrByRle | 0.361 | 0.008 | 0.371 | |
easyLoad_FUN | 0.065 | 0.002 | 0.067 | |
easyLoad_IDRmerged | 0.050 | 0.002 | 0.053 | |
easyLoad_bed | 0.155 | 0.002 | 0.157 | |
easyLoad_broadPeak | 0.048 | 0.002 | 0.050 | |
easyLoad_narrowPeak | 0.047 | 0.002 | 0.049 | |
easyLoad_seacr | 0.049 | 0.001 | 0.050 | |
expandCigar | 0.167 | 0.018 | 0.188 | |
findMaxPos | 0.037 | 0.007 | 0.045 | |
fragLen_calcStranded | 1.866 | 0.037 | 1.917 | |
fragLen_fromMacs2Xls | 0.002 | 0.001 | 0.003 | |
getReadLength | 0.060 | 0.004 | 0.064 | |
get_mapped_reads | 0.011 | 0.000 | 0.012 | |
ggellipse | 0.610 | 0.008 | 0.622 | |
harmonize_seqlengths | 0.148 | 0.012 | 0.161 | |
make_clustering_matrix | 0.056 | 0.003 | 0.059 | |
merge_clusters | 3.678 | 0.042 | 3.744 | |
prepare_fetch_GRanges | 0.033 | 0.002 | 0.035 | |
prepare_fetch_GRanges_names | 0.096 | 0.003 | 0.099 | |
prepare_fetch_GRanges_width | 0.032 | 0.002 | 0.035 | |
quantileGRangesWidth | 0.004 | 0.002 | 0.005 | |
reorder_clusters_hclust | 2.075 | 0.021 | 2.105 | |
reorder_clusters_manual | 1.141 | 0.014 | 1.165 | |
reorder_clusters_stepdown | 2.121 | 0.038 | 2.189 | |
reverse_clusters | 2.344 | 0.045 | 2.397 | |
safeBrew | 0.029 | 0.005 | 0.035 | |
split_cluster | 1.968 | 0.024 | 2.005 | |
ssvAnnotateSubjectGRanges | 1.157 | 0.029 | 1.190 | |
ssvConsensusIntervalSets | 0.407 | 0.012 | 0.422 | |
ssvFactorizeMembTable | 0.016 | 0.004 | 0.018 | |
ssvFeatureBars | 0.617 | 0.007 | 0.629 | |
ssvFeatureBinaryHeatmap | 7.664 | 0.720 | 8.447 | |
ssvFeatureEuler | 0.601 | 0.013 | 0.620 | |
ssvFeaturePie | 0.531 | 0.016 | 0.552 | |
ssvFeatureUpset | 2.886 | 0.073 | 2.992 | |
ssvFeatureVenn | 1.030 | 0.014 | 1.051 | |
ssvFetchBam | 7.203 | 0.336 | 7.596 | |
ssvFetchBamPE | 2.422 | 0.242 | 2.689 | |
ssvFetchBamPE.RNA | 1.810 | 0.039 | 1.864 | |
ssvFetchBigwig | 1.659 | 0.047 | 1.719 | |
ssvFetchGRanges | 0.909 | 0.013 | 0.928 | |
ssvFetchSignal | 1.690 | 0.059 | 1.761 | |
ssvMakeMembTable-methods | 0.606 | 0.013 | 0.623 | |
ssvOverlapIntervalSets | 0.300 | 0.011 | 0.313 | |
ssvSignalBandedQuantiles | 4.044 | 0.079 | 4.155 | |
ssvSignalClustering | 2.915 | 0.068 | 3.006 | |
ssvSignalHeatmap.ClusterBars | 3.631 | 0.093 | 3.774 | |
ssvSignalHeatmap | 3.965 | 0.053 | 4.042 | |
ssvSignalLineplot | 2.499 | 0.023 | 2.542 | |
ssvSignalLineplotAgg | 0.842 | 0.011 | 0.859 | |
ssvSignalScatterplot | 0.921 | 0.020 | 0.954 | |
viewGRangesWinSample_dt | 1.463 | 0.051 | 1.525 | |
viewGRangesWinSummary_dt | 1.362 | 0.056 | 1.427 | |
within_clust_sort | 1.649 | 0.031 | 1.694 | |