Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:31 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1873/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.19.3 (landing page) Joseph R Boyd
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: seqsetvis |
Version: 1.19.3 |
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/site-library --timings seqsetvis_1.19.3.tar.gz |
StartedAt: 2023-04-11 23:31:25 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 23:41:20 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 595.1 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/site-library --timings seqsetvis_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-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 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.19.3’ * 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 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 ... NOTE ssvSignalBandedQuantiles: no visible binding for global variable ‘x’ ssvSignalLineplotAgg: no visible binding for global variable ‘y’ Undefined global functions or variables: x y * 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 7.711 0.303 8.016 ssvFetchBam 6.424 0.093 6.498 ssvSignalBandedQuantiles 5.022 0.035 4.929 * 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/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 4.3.0 alpha (2023-04-03 r84154) Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-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 251.194 2.208 250.092
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 1.808 | 0.139 | 1.912 | |
append_ynorm | 0.053 | 0.004 | 0.032 | |
applySpline | 0.506 | 0.040 | 0.509 | |
assemble_heatmap_cluster_bars | 0.774 | 0.028 | 0.769 | |
calc_norm_factors | 0.023 | 0.000 | 0.012 | |
centerAtMax | 0.363 | 0.016 | 0.332 | |
centerFixedSizeGRanges | 0.163 | 0.004 | 0.167 | |
centerGRangesAtMax | 0.396 | 0.004 | 0.367 | |
clusteringKmeans | 0.025 | 0.000 | 0.015 | |
clusteringKmeansNestedHclust | 0.029 | 0.002 | 0.021 | |
col2hex | 0.000 | 0.001 | 0.001 | |
collapse_gr | 0.731 | 0.008 | 0.742 | |
convert_collapsed_coord | 0.220 | 0.013 | 0.234 | |
copy_clust_info | 1.765 | 0.040 | 1.727 | |
crossCorrByRle | 0.413 | 0.008 | 0.422 | |
easyLoad_FUN | 0.047 | 0.004 | 0.051 | |
easyLoad_IDRmerged | 0.046 | 0.008 | 0.054 | |
easyLoad_bed | 0.118 | 0.004 | 0.122 | |
easyLoad_broadPeak | 0.036 | 0.004 | 0.040 | |
easyLoad_narrowPeak | 0.038 | 0.000 | 0.038 | |
easyLoad_seacr | 0.043 | 0.000 | 0.044 | |
expandCigar | 0.178 | 0.000 | 0.160 | |
fragLen_calcStranded | 1.686 | 0.060 | 1.740 | |
fragLen_fromMacs2Xls | 0.003 | 0.000 | 0.003 | |
getReadLength | 0.050 | 0.004 | 0.054 | |
get_mapped_reads | 0.006 | 0.004 | 0.009 | |
ggellipse | 0.574 | 0.004 | 0.578 | |
harmonize_seqlengths | 0.112 | 0.000 | 0.112 | |
make_clustering_matrix | 0.051 | 0.000 | 0.039 | |
merge_clusters | 4.265 | 0.184 | 4.355 | |
prepare_fetch_GRanges | 0.028 | 0.000 | 0.028 | |
prepare_fetch_GRanges_names | 0.066 | 0.008 | 0.074 | |
prepare_fetch_GRanges_width | 0.026 | 0.000 | 0.026 | |
quantileGRangesWidth | 0.000 | 0.002 | 0.001 | |
reorder_clusters_hclust | 1.813 | 0.030 | 1.798 | |
reorder_clusters_manual | 0.938 | 0.021 | 0.918 | |
reorder_clusters_stepdown | 1.762 | 0.016 | 1.732 | |
reverse_clusters | 1.939 | 0.036 | 1.885 | |
safeBrew | 0.023 | 0.000 | 0.023 | |
split_cluster | 1.736 | 0.027 | 1.669 | |
ssvConsensusIntervalSets | 0.346 | 0.008 | 0.354 | |
ssvFactorizeMembTable | 0.014 | 0.000 | 0.015 | |
ssvFeatureBars | 0.640 | 0.000 | 0.641 | |
ssvFeatureBinaryHeatmap | 7.711 | 0.303 | 8.016 | |
ssvFeatureEuler | 0.552 | 0.000 | 0.552 | |
ssvFeaturePie | 0.580 | 0.008 | 0.588 | |
ssvFeatureUpset | 2.668 | 0.012 | 2.681 | |
ssvFeatureVenn | 0.685 | 0.004 | 0.689 | |
ssvFetchBam | 6.424 | 0.093 | 6.498 | |
ssvFetchBamPE | 2.147 | 0.015 | 2.164 | |
ssvFetchBigwig | 1.448 | 0.003 | 1.452 | |
ssvFetchGRanges | 0.777 | 0.000 | 0.776 | |
ssvFetchSignal | 1.614 | 0.011 | 1.626 | |
ssvMakeMembTable-methods | 0.595 | 0.008 | 0.603 | |
ssvOverlapIntervalSets | 0.275 | 0.002 | 0.277 | |
ssvSignalBandedQuantiles | 5.022 | 0.035 | 4.929 | |
ssvSignalClustering | 2.213 | 0.004 | 2.120 | |
ssvSignalHeatmap.ClusterBars | 4.255 | 0.164 | 4.237 | |
ssvSignalHeatmap | 3.594 | 0.056 | 3.415 | |
ssvSignalLineplot | 2.235 | 0.004 | 2.233 | |
ssvSignalLineplotAgg | 1.110 | 0.000 | 1.091 | |
ssvSignalScatterplot | 0.875 | 0.000 | 0.828 | |
viewGRangesWinSample_dt | 1.359 | 0.012 | 1.366 | |
viewGRangesWinSummary_dt | 1.189 | 0.008 | 1.174 | |
within_clust_sort | 1.664 | 0.020 | 1.627 | |