Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:50 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the seqsetvis package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1841/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.19.2 (landing page) Joseph R Boyd
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: seqsetvis |
Version: 1.19.2 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings seqsetvis_1.19.2.tar.gz |
StartedAt: 2023-02-28 15:11:34 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 15:24:04 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 750.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: seqsetvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings seqsetvis_1.19.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.19.2’ * 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 R 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 ... NOTE ssvSignalBandedQuantiles: no visible binding for global variable ‘x’ Undefined global functions or variables: x * 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 9.794 0.244 10.039 ssvFetchBam 9.453 0.076 9.528 ssvSignalBandedQuantiles 6.794 0.024 6.804 ssvSignalHeatmap 5.114 0.016 5.094 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘seqsetvis_overview.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck/00check.log’ for details.
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 1182 ] > > proc.time() user system elapsed 328.152 2.116 329.990
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 2.627 | 0.120 | 2.741 | |
append_ynorm | 0.042 | 0.005 | 0.043 | |
applySpline | 0.664 | 0.012 | 0.670 | |
assemble_heatmap_cluster_bars | 1.001 | 0.004 | 1.000 | |
calc_norm_factors | 0.017 | 0.000 | 0.016 | |
centerAtMax | 0.384 | 0.000 | 0.379 | |
centerFixedSizeGRanges | 0.177 | 0.004 | 0.180 | |
centerGRangesAtMax | 0.528 | 0.000 | 0.524 | |
clusteringKmeans | 0.021 | 0.004 | 0.021 | |
clusteringKmeansNestedHclust | 0.033 | 0.000 | 0.031 | |
col2hex | 0.002 | 0.000 | 0.001 | |
collapse_gr | 0.938 | 0.004 | 0.941 | |
convert_collapsed_coord | 0.272 | 0.000 | 0.272 | |
copy_clust_info | 2.377 | 0.020 | 2.388 | |
crossCorrByRle | 0.450 | 0.008 | 0.462 | |
easyLoad_FUN | 0.070 | 0.000 | 0.071 | |
easyLoad_IDRmerged | 0.069 | 0.004 | 0.073 | |
easyLoad_bed | 0.174 | 0.000 | 0.174 | |
easyLoad_broadPeak | 0.052 | 0.000 | 0.053 | |
easyLoad_narrowPeak | 0.049 | 0.004 | 0.055 | |
easyLoad_seacr | 0.058 | 0.000 | 0.059 | |
expandCigar | 0.214 | 0.004 | 0.216 | |
fragLen_calcStranded | 3.350 | 0.047 | 3.396 | |
fragLen_fromMacs2Xls | 0.003 | 0.001 | 0.003 | |
getReadLength | 0.064 | 0.007 | 0.071 | |
get_mapped_reads | 0.007 | 0.004 | 0.012 | |
ggellipse | 0.796 | 0.004 | 0.801 | |
harmonize_seqlengths | 0.149 | 0.000 | 0.149 | |
make_clustering_matrix | 0.061 | 0.000 | 0.058 | |
merge_clusters | 4.725 | 0.073 | 4.785 | |
prepare_fetch_GRanges | 0.039 | 0.000 | 0.039 | |
prepare_fetch_GRanges_names | 0.11 | 0.00 | 0.11 | |
prepare_fetch_GRanges_width | 0.040 | 0.000 | 0.039 | |
quantileGRangesWidth | 0.002 | 0.000 | 0.002 | |
reorder_clusters_hclust | 2.662 | 0.016 | 2.672 | |
reorder_clusters_manual | 1.382 | 0.016 | 1.392 | |
reorder_clusters_stepdown | 2.675 | 0.008 | 2.676 | |
reverse_clusters | 2.843 | 0.020 | 2.848 | |
safeBrew | 0.028 | 0.004 | 0.031 | |
split_cluster | 2.432 | 0.012 | 2.428 | |
ssvConsensusIntervalSets | 0.505 | 0.024 | 0.529 | |
ssvFactorizeMembTable | 0.018 | 0.000 | 0.018 | |
ssvFeatureBars | 0.964 | 0.020 | 0.984 | |
ssvFeatureBinaryHeatmap | 9.794 | 0.244 | 10.039 | |
ssvFeatureEuler | 0.751 | 0.004 | 0.756 | |
ssvFeaturePie | 0.805 | 0.000 | 0.805 | |
ssvFeatureUpset | 3.878 | 0.024 | 3.902 | |
ssvFeatureVenn | 0.974 | 0.000 | 0.975 | |
ssvFetchBam | 9.453 | 0.076 | 9.528 | |
ssvFetchBamPE | 2.921 | 0.008 | 2.933 | |
ssvFetchBigwig | 2.011 | 0.012 | 2.023 | |
ssvFetchGRanges | 1.134 | 0.020 | 1.154 | |
ssvFetchSignal | 2.233 | 0.008 | 2.241 | |
ssvMakeMembTable-methods | 0.745 | 0.004 | 0.749 | |
ssvOverlapIntervalSets | 0.337 | 0.000 | 0.337 | |
ssvSignalBandedQuantiles | 6.794 | 0.024 | 6.804 | |
ssvSignalClustering | 2.941 | 0.024 | 2.951 | |
ssvSignalHeatmap.ClusterBars | 4.305 | 0.012 | 4.292 | |
ssvSignalHeatmap | 5.114 | 0.016 | 5.094 | |
ssvSignalLineplot | 3.42 | 0.00 | 3.42 | |
ssvSignalLineplotAgg | 1.546 | 0.032 | 1.576 | |
ssvSignalScatterplot | 1.192 | 0.016 | 1.204 | |
viewGRangesWinSample_dt | 1.972 | 0.004 | 1.976 | |
viewGRangesWinSummary_dt | 1.764 | 0.000 | 1.763 | |
within_clust_sort | 2.114 | 0.000 | 2.104 | |