Joseph R Boyd
| Snapshot Date: 2023-09-20 14:00:09 -0400 (Wed, 20 Sep 2023) |
| git_url: https://git.bioconductor.org/packages/seqsetvis |
| git_branch: RELEASE_3_17 |
| git_last_commit: 99963de |
| git_last_commit_date: 2023-04-25 11:00:32 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-21 11:35:47 -0400 (Thu, 21 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 1893/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqsetvis 1.20.0 (landing page) Joseph R Boyd
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | NA | |||||||||
|
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: 1.20.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings seqsetvis_1.20.0.tar.gz |
| StartedAt: 2023-09-21 06:53:18 -0400 (Thu, 21 Sep 2023) |
| EndedAt: 2023-09-21 07:01:53 -0400 (Thu, 21 Sep 2023) |
| EllapsedTime: 515.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqsetvis.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings seqsetvis_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'seqsetvis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqsetvis' version '1.20.0'
* 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 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'
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 5.83 0.41 6.25
merge_clusters 5.66 0.00 6.42
add_cluster_annotation 3.65 0.10 7.22
reorder_clusters_hclust 2.61 0.02 9.50
copy_clust_info 2.46 0.01 7.61
append_ynorm 0.06 0.01 5.69
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck/00check.log'
for details.
seqsetvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL seqsetvis ### ############################################################################## ############################################################################## * installing to library 'F:/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 version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 37 | PASS 716 ] ══ Skipped tests (37) ══════════════════════════════════════════════════════════ • On Windows (37): 'test_anchor.R:108:5', 'test_anchor.R:163:5', 'test_fetchBam.R:98:5', 'test_fetchBam.R:142:5', 'test_fetchBam.R:170:5', 'test_fetchBam.R:201:5', 'test_fetchBw.R:17:5', 'test_fetchBw.R:32:5', 'test_fetchBw.R:46:5', 'test_fetchBw.R:63:5', 'test_fetchBw.R:73:5', 'test_fetchBw.R:86:5', 'test_fetchBw.R:97:5', 'test_fetchBw.R:108:5', 'test_fetchBw.R:120:5', 'test_fetchBw.R:143:5', 'test_fetchBw.R:153:5', 'test_fetchBw.R:165:5', 'test_fetchBw.R:175:5', 'test_fetchBw.R:190:5', 'test_fetchBw.R:205:5', 'test_fetchBw.R:220:5', 'test_fetchBw_dt.R:15:5', 'test_fetchBw_dt.R:31:5', 'test_fetchBw_dt.R:46:5', 'test_fetchBw_dt.R:64:5', 'test_fetchBw_dt.R:74:5', 'test_fetchBw_dt.R:87:5', 'test_fetchBw_dt.R:98:5', 'test_fetchBw_dt.R:109:5', 'test_fetchBw_dt.R:121:5', 'test_fetchBw_dt.R:133:5', 'test_fetch_parallel.R:16:5', 'test_fetch_parallel.R:44:5', 'test_force_skip.R:33:5', 'test_viewGrangesWin_sample_vs_summary.R:115:5', 'test_viewGrangesWin_sample_vs_summary.R:136:5' [ FAIL 0 | WARN 0 | SKIP 37 | PASS 716 ] > > proc.time() user system elapsed 176.32 3.42 180.01
seqsetvis.Rcheck/seqsetvis-Ex.timings
| name | user | system | elapsed | |
| add_cluster_annotation | 3.65 | 0.10 | 7.22 | |
| append_ynorm | 0.06 | 0.01 | 5.69 | |
| applySpline | 0.67 | 0.05 | 4.69 | |
| assemble_heatmap_cluster_bars | 1.14 | 0.03 | 2.15 | |
| calc_norm_factors | 0.02 | 0.00 | 0.02 | |
| centerAtMax | 0.33 | 0.00 | 0.33 | |
| centerFixedSizeGRanges | 0.17 | 0.00 | 0.17 | |
| centerGRangesAtMax | 0.36 | 0.01 | 0.37 | |
| clusteringKmeans | 0.00 | 0.02 | 0.02 | |
| clusteringKmeansNestedHclust | 0.01 | 0.00 | 0.01 | |
| col2hex | 0.02 | 0.00 | 0.02 | |
| collapse_gr | 0.98 | 0.03 | 1.05 | |
| convert_collapsed_coord | 0.18 | 0.05 | 0.21 | |
| copy_clust_info | 2.46 | 0.01 | 7.61 | |
| crossCorrByRle | 0.54 | 0.00 | 0.60 | |
| easyLoad_FUN | 0.06 | 0.00 | 0.54 | |
| easyLoad_IDRmerged | 0.06 | 0.00 | 1.27 | |
| easyLoad_bed | 0.2 | 0.0 | 0.2 | |
| easyLoad_broadPeak | 0.10 | 0.00 | 0.41 | |
| easyLoad_narrowPeak | 0.08 | 0.00 | 0.34 | |
| easyLoad_seacr | 0.09 | 0.00 | 0.23 | |
| expandCigar | 0.25 | 0.01 | 1.94 | |
| fragLen_calcStranded | 2.56 | 0.03 | 3.27 | |
| fragLen_fromMacs2Xls | 0.02 | 0.00 | 0.15 | |
| getReadLength | 0.08 | 0.00 | 0.19 | |
| get_mapped_reads | 0.01 | 0.00 | 0.02 | |
| ggellipse | 0.91 | 0.02 | 0.92 | |
| harmonize_seqlengths | 0.14 | 0.05 | 0.19 | |
| make_clustering_matrix | 0.12 | 0.01 | 2.25 | |
| merge_clusters | 5.66 | 0.00 | 6.42 | |
| prepare_fetch_GRanges | 0.03 | 0.00 | 0.03 | |
| prepare_fetch_GRanges_names | 0.13 | 0.00 | 0.12 | |
| prepare_fetch_GRanges_width | 0.04 | 0.00 | 0.05 | |
| quantileGRangesWidth | 0 | 0 | 0 | |
| reorder_clusters_hclust | 2.61 | 0.02 | 9.50 | |
| reorder_clusters_manual | 1.00 | 0.00 | 1.23 | |
| reorder_clusters_stepdown | 1.64 | 0.00 | 1.65 | |
| reverse_clusters | 1.81 | 0.01 | 1.84 | |
| safeBrew | 0.04 | 0.00 | 0.03 | |
| split_cluster | 1.62 | 0.07 | 1.70 | |
| ssvConsensusIntervalSets | 0.31 | 0.00 | 0.32 | |
| ssvFactorizeMembTable | 0.02 | 0.00 | 0.01 | |
| ssvFeatureBars | 1.34 | 0.04 | 1.39 | |
| ssvFeatureBinaryHeatmap | 5.83 | 0.41 | 6.25 | |
| ssvFeatureEuler | 0.49 | 0.06 | 0.55 | |
| ssvFeaturePie | 0.57 | 0.02 | 0.59 | |
| ssvFeatureUpset | 2.64 | 0.00 | 2.64 | |
| ssvFeatureVenn | 0.60 | 0.02 | 0.61 | |
| ssvFetchBam | 0 | 0 | 0 | |
| ssvFetchBamPE | 0 | 0 | 0 | |
| ssvFetchBigwig | 0 | 0 | 0 | |
| ssvFetchGRanges | 0.72 | 0.00 | 0.72 | |
| ssvFetchSignal | 1.39 | 0.03 | 1.42 | |
| ssvMakeMembTable-methods | 0.48 | 0.00 | 0.48 | |
| ssvOverlapIntervalSets | 0.22 | 0.02 | 0.24 | |
| ssvSignalBandedQuantiles | 4.84 | 0.04 | 4.90 | |
| ssvSignalClustering | 1.91 | 0.00 | 1.91 | |
| ssvSignalHeatmap.ClusterBars | 2.98 | 0.03 | 3.02 | |
| ssvSignalHeatmap | 3.48 | 0.08 | 3.56 | |
| ssvSignalLineplot | 2.99 | 0.04 | 3.03 | |
| ssvSignalLineplotAgg | 1.06 | 0.05 | 1.11 | |
| ssvSignalScatterplot | 0.95 | 0.00 | 0.95 | |
| viewGRangesWinSample_dt | 1.07 | 0.02 | 1.08 | |
| viewGRangesWinSummary_dt | 0.97 | 0.03 | 1.00 | |
| within_clust_sort | 1.50 | 0.01 | 1.53 | |