Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 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" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 12.7.4 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: /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_1.24.0.tar.gz |
StartedAt: 2024-07-08 11:45:13 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 12:11:02 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 1548.4 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.24.0’ * 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 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 ssvFetchBam 16.230 0.543 20.031 ssvFeatureBinaryHeatmap 9.586 0.871 12.175 ssvSignalBandedQuantiles 8.933 0.168 11.956 ssvSignalHeatmap 8.385 0.207 10.551 merge_clusters 8.283 0.115 10.221 ssvSignalHeatmap.ClusterBars 7.234 0.120 9.431 add_cluster_annotation 6.077 0.222 7.580 ssvFeatureUpset 6.179 0.072 7.532 reverse_clusters 5.805 0.060 7.545 ssvSignalLineplot 5.423 0.091 6.926 ssvFetchBamPE 4.833 0.385 6.042 reorder_clusters_hclust 4.748 0.095 5.712 ssvSignalClustering 4.681 0.109 5.517 reorder_clusters_stepdown 4.732 0.047 5.989 fragLen_calcStranded 4.367 0.081 5.260 copy_clust_info 3.928 0.041 5.131 * 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 *** 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-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 1266 ] > > proc.time() user system elapsed 642.847 12.183 760.465
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 6.077 | 0.222 | 7.580 | |
append_ynorm | 0.077 | 0.016 | 0.110 | |
applyMovingAverage | 1.758 | 0.170 | 2.287 | |
applySpline | 0.751 | 0.009 | 0.880 | |
assemble_heatmap_cluster_bars | 1.790 | 0.019 | 2.105 | |
calc_norm_factors | 0.031 | 0.001 | 0.034 | |
centerAtMax | 0.666 | 0.016 | 0.800 | |
centerFixedSizeGRanges | 0.308 | 0.014 | 0.370 | |
centerGRangesAtMax | 0.833 | 0.012 | 0.981 | |
clusteringKmeans | 0.035 | 0.005 | 0.050 | |
clusteringKmeansNestedHclust | 0.050 | 0.007 | 0.065 | |
col2hex | 0.003 | 0.001 | 0.003 | |
collapse_gr | 1.679 | 0.033 | 2.004 | |
convert_collapsed_coord | 0.450 | 0.018 | 0.555 | |
copy_clust_info | 3.928 | 0.041 | 5.131 | |
crossCorrByRle | 0.796 | 0.014 | 1.045 | |
easyLoad_FUN | 0.118 | 0.003 | 0.145 | |
easyLoad_IDRmerged | 0.102 | 0.004 | 0.133 | |
easyLoad_bed | 0.340 | 0.005 | 0.412 | |
easyLoad_broadPeak | 0.102 | 0.002 | 0.130 | |
easyLoad_narrowPeak | 0.098 | 0.003 | 0.122 | |
easyLoad_seacr | 0.106 | 0.003 | 0.135 | |
expandCigar | 0.372 | 0.033 | 0.518 | |
findMaxPos | 0.033 | 0.009 | 0.056 | |
fragLen_calcStranded | 4.367 | 0.081 | 5.260 | |
fragLen_fromMacs2Xls | 0.003 | 0.001 | 0.006 | |
getReadLength | 0.124 | 0.008 | 0.161 | |
get_mapped_reads | 0.019 | 0.001 | 0.022 | |
ggellipse | 1.338 | 0.015 | 1.583 | |
harmonize_seqlengths | 0.201 | 0.015 | 0.257 | |
make_clustering_matrix | 0.109 | 0.003 | 0.129 | |
merge_clusters | 8.283 | 0.115 | 10.221 | |
prepare_fetch_GRanges | 0.069 | 0.003 | 0.089 | |
prepare_fetch_GRanges_names | 0.195 | 0.005 | 0.239 | |
prepare_fetch_GRanges_width | 0.069 | 0.003 | 0.084 | |
quantileGRangesWidth | 0.003 | 0.000 | 0.009 | |
reorder_clusters_hclust | 4.748 | 0.095 | 5.712 | |
reorder_clusters_manual | 2.403 | 0.027 | 3.100 | |
reorder_clusters_stepdown | 4.732 | 0.047 | 5.989 | |
reverse_clusters | 5.805 | 0.060 | 7.545 | |
safeBrew | 0.048 | 0.006 | 0.062 | |
split_cluster | 4.182 | 0.031 | 4.974 | |
ssvConsensusIntervalSets | 0.699 | 0.018 | 0.862 | |
ssvFactorizeMembTable | 0.029 | 0.008 | 0.047 | |
ssvFeatureBars | 1.275 | 0.012 | 1.547 | |
ssvFeatureBinaryHeatmap | 9.586 | 0.871 | 12.175 | |
ssvFeatureEuler | 1.296 | 0.040 | 1.603 | |
ssvFeaturePie | 1.444 | 0.030 | 1.779 | |
ssvFeatureUpset | 6.179 | 0.072 | 7.532 | |
ssvFeatureVenn | 2.265 | 0.023 | 2.781 | |
ssvFetchBam | 16.230 | 0.543 | 20.031 | |
ssvFetchBamPE | 4.833 | 0.385 | 6.042 | |
ssvFetchBigwig | 3.435 | 0.042 | 4.016 | |
ssvFetchGRanges | 1.894 | 0.019 | 2.193 | |
ssvFetchSignal | 3.465 | 0.091 | 3.706 | |
ssvMakeMembTable-methods | 1.142 | 0.023 | 1.254 | |
ssvOverlapIntervalSets | 0.514 | 0.018 | 0.568 | |
ssvSignalBandedQuantiles | 8.933 | 0.168 | 11.956 | |
ssvSignalClustering | 4.681 | 0.109 | 5.517 | |
ssvSignalHeatmap.ClusterBars | 7.234 | 0.120 | 9.431 | |
ssvSignalHeatmap | 8.385 | 0.207 | 10.551 | |
ssvSignalLineplot | 5.423 | 0.091 | 6.926 | |
ssvSignalLineplotAgg | 1.842 | 0.017 | 2.107 | |
ssvSignalScatterplot | 2.013 | 0.025 | 2.307 | |
viewGRangesWinSample_dt | 3.142 | 0.098 | 3.897 | |
viewGRangesWinSummary_dt | 2.982 | 0.096 | 3.794 | |
within_clust_sort | 3.586 | 0.047 | 4.504 | |