Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:42 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 1914/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqsetvis 1.25.4 (landing page) Joseph R Boyd
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.25.4 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqsetvis_1.25.4.tar.gz |
StartedAt: 2024-10-03 01:17:49 -0400 (Thu, 03 Oct 2024) |
EndedAt: 2024-10-03 01:27:16 -0400 (Thu, 03 Oct 2024) |
EllapsedTime: 567.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: seqsetvis.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqsetvis_1.25.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘seqsetvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqsetvis’ version ‘1.25.4’ * 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 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 7.584 0.231 7.818 ssvFetchBam 5.683 0.040 5.670 * 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 ... ERROR Error(s) in re-building vignettes: ... Warning in gzfile(file, mode) : cannot open compressed file '/tmp/RtmpNTlPn9/libloc_190_c838c4f63143a0a3.rds', probable reason 'No space left on device' Error in gzfile(file, mode) : cannot open the connection Calls: <Anonymous> ... rownames -> %||% -> <Anonymous> -> saveRDS -> gzfile Execution halted * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Fatal error: cannot create 'R_TempDir' * DONE Status: 2 ERRORs, 1 WARNING See ‘/home/biocbuild/bbs-3.20-bioc/meat/seqsetvis.Rcheck/00check.log’ for details.
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 (2024-06-14) -- "Race for Your Life" 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 27 | SKIP 0 | PASS 1284 ] [ FAIL 0 | WARN 27 | SKIP 0 | PASS 1284 ] > > proc.time() user system elapsed 262.532 1.377 259.465
seqsetvis.Rcheck/seqsetvis-Ex.timings
name | user | system | elapsed | |
add_cluster_annotation | 3.185 | 0.198 | 3.346 | |
append_ynorm | 0.072 | 0.007 | 0.047 | |
applyMovingAverage | 0.706 | 0.000 | 0.699 | |
applySpline | 0.384 | 0.003 | 0.337 | |
assemble_heatmap_cluster_bars | 0.810 | 0.000 | 0.751 | |
calc_norm_factors | 0.034 | 0.001 | 0.023 | |
centerAtMax | 0.357 | 0.003 | 0.263 | |
centerFixedSizeGRanges | 0.15 | 0.00 | 0.15 | |
centerGRangesAtMax | 0.421 | 0.003 | 0.362 | |
clusteringKmeans | 0.040 | 0.001 | 0.026 | |
clusteringKmeansNestedHclust | 0.057 | 0.001 | 0.030 | |
col2hex | 0.001 | 0.000 | 0.001 | |
collapse_gr | 0.681 | 0.039 | 0.720 | |
convert_collapsed_coord | 0.196 | 0.006 | 0.202 | |
copy_clust_info | 1.722 | 0.031 | 1.650 | |
crossCorrByRle | 0.318 | 0.001 | 0.319 | |
easyLoad_FUN | 0.071 | 0.000 | 0.071 | |
easyLoad_IDRmerged | 0.043 | 0.000 | 0.044 | |
easyLoad_bed | 0.123 | 0.001 | 0.124 | |
easyLoad_broadPeak | 0.036 | 0.000 | 0.036 | |
easyLoad_narrowPeak | 0.035 | 0.000 | 0.035 | |
easyLoad_seacr | 0.038 | 0.001 | 0.039 | |
expandCigar | 0.170 | 0.003 | 0.154 | |
findMaxPos | 0.038 | 0.003 | 0.033 | |
fragLen_calcStranded | 1.640 | 0.001 | 1.623 | |
fragLen_fromMacs2Xls | 0.003 | 0.000 | 0.003 | |
getReadLength | 0.055 | 0.000 | 0.056 | |
get_mapped_reads | 0.008 | 0.000 | 0.008 | |
ggellipse | 0.556 | 0.002 | 0.558 | |
harmonize_seqlengths | 0.107 | 0.001 | 0.108 | |
make_clustering_matrix | 0.086 | 0.000 | 0.066 | |
merge_clusters | 3.457 | 0.052 | 3.362 | |
prepare_fetch_GRanges | 0.026 | 0.002 | 0.029 | |
prepare_fetch_GRanges_names | 0.072 | 0.005 | 0.078 | |
prepare_fetch_GRanges_width | 0.027 | 0.001 | 0.028 | |
quantileGRangesWidth | 0.003 | 0.000 | 0.003 | |
reorder_clusters_hclust | 1.901 | 0.020 | 1.875 | |
reorder_clusters_manual | 1.027 | 0.051 | 1.039 | |
reorder_clusters_stepdown | 1.924 | 0.027 | 1.890 | |
reverse_clusters | 2.235 | 0.014 | 2.152 | |
safeBrew | 0.024 | 0.001 | 0.025 | |
split_cluster | 2.929 | 0.265 | 3.099 | |
ssvAnnotateSubjectGRanges | 0.960 | 0.015 | 0.975 | |
ssvConsensusIntervalSets | 0.345 | 0.005 | 0.350 | |
ssvFactorizeMembTable | 0.015 | 0.000 | 0.015 | |
ssvFeatureBars | 0.552 | 0.013 | 0.565 | |
ssvFeatureBinaryHeatmap | 7.584 | 0.231 | 7.818 | |
ssvFeatureEuler | 0.731 | 0.005 | 0.736 | |
ssvFeaturePie | 0.456 | 0.001 | 0.458 | |
ssvFeatureUpset | 2.317 | 0.001 | 2.319 | |
ssvFeatureVenn | 0.820 | 0.012 | 0.833 | |
ssvFetchBam | 5.683 | 0.040 | 5.670 | |
ssvFetchBamPE | 1.897 | 0.061 | 1.961 | |
ssvFetchBamPE.RNA | 1.356 | 0.009 | 1.313 | |
ssvFetchBigwig | 1.286 | 0.042 | 1.325 | |
ssvFetchGRanges | 0.710 | 0.024 | 0.733 | |
ssvFetchSignal | 1.415 | 0.009 | 1.423 | |
ssvMakeMembTable-methods | 0.475 | 0.004 | 0.480 | |
ssvOverlapIntervalSets | 0.216 | 0.003 | 0.220 | |
ssvSignalBandedQuantiles | 3.584 | 0.045 | 3.509 | |
ssvSignalClustering | 2.510 | 0.005 | 2.340 | |
ssvSignalHeatmap.ClusterBars | 3.105 | 0.020 | 2.927 | |
ssvSignalHeatmap | 3.726 | 0.028 | 3.526 | |
ssvSignalLineplot | 2.044 | 0.001 | 2.039 | |
ssvSignalLineplotAgg | 0.907 | 0.018 | 0.907 | |
ssvSignalScatterplot | 0.875 | 0.031 | 0.863 | |
viewGRangesWinSample_dt | 1.235 | 0.022 | 1.252 | |
viewGRangesWinSummary_dt | 1.153 | 0.003 | 1.132 | |
within_clust_sort | 1.453 | 0.055 | 1.449 | |