Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-09-21 11:36:38 -0400 (Thu, 21 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (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 1893/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.20.0  (landing page)
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)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    NA  

CHECK results for seqsetvis on merida1


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.

raw results


Summary

Package: seqsetvis
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2023-09-21 08:34:29 -0400 (Thu, 21 Sep 2023)
EndedAt: 2023-09-21 09:02:06 -0400 (Thu, 21 Sep 2023)
EllapsedTime: 1657.2 seconds
RetCode: 0
Status:   OK  
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.20.0’
* 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 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’
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
ssvFetchBam                  15.080  0.799  23.028
ssvSignalBandedQuantiles     11.453  0.257  17.067
ssvFeatureBinaryHeatmap       8.338  1.101  14.357
merge_clusters                8.383  0.190  12.560
ssvSignalHeatmap              7.956  0.175  11.249
ssvSignalHeatmap.ClusterBars  6.792  0.172   9.549
ssvFeatureUpset               6.291  0.135   9.326
ssvSignalLineplot             5.589  0.113   8.011
add_cluster_annotation        5.056  0.293   7.531
ssvFetchBamPE                 4.528  0.491   7.317
ssvSignalClustering           4.677  0.129   7.086
reverse_clusters              4.554  0.096   6.741
reorder_clusters_hclust       4.278  0.082   6.384
reorder_clusters_stepdown     4.273  0.075   6.409
fragLen_calcStranded          4.084  0.116   6.227
split_cluster                 3.908  0.089   5.691
copy_clust_info               3.765  0.074   5.584
ssvFetchSignal                3.518  0.132   5.225
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/seqsetvis.Rcheck/00check.log’
for details.



Installation output

seqsetvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)

Tests output

seqsetvis.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
543.568  16.693 782.136 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
add_cluster_annotation5.0560.2937.531
append_ynorm0.0580.0060.088
applySpline1.0200.0201.475
assemble_heatmap_cluster_bars1.5940.0422.395
calc_norm_factors0.0250.0020.041
centerAtMax0.6170.0230.924
centerFixedSizeGRanges0.2960.0180.449
centerGRangesAtMax0.7860.0201.182
clusteringKmeans0.0270.0040.045
clusteringKmeansNestedHclust0.0440.0060.073
col2hex0.0020.0010.006
collapse_gr1.5240.0502.259
convert_collapsed_coord0.4040.0240.606
copy_clust_info3.7650.0745.584
crossCorrByRle0.7590.0371.191
easyLoad_FUN0.1110.0040.166
easyLoad_IDRmerged0.1150.0060.177
easyLoad_bed0.2900.0050.427
easyLoad_broadPeak0.0810.0040.120
easyLoad_narrowPeak0.0790.0020.112
easyLoad_seacr0.0940.0040.141
expandCigar0.3360.0340.546
fragLen_calcStranded4.0840.1166.227
fragLen_fromMacs2Xls0.0030.0010.005
getReadLength0.1090.0110.183
get_mapped_reads0.0170.0010.029
ggellipse1.3190.0281.974
harmonize_seqlengths0.2050.0160.318
make_clustering_matrix0.0920.0030.114
merge_clusters 8.383 0.19012.560
prepare_fetch_GRanges0.0640.0050.095
prepare_fetch_GRanges_names0.1820.0090.280
prepare_fetch_GRanges_width0.0660.0040.097
quantileGRangesWidth0.0030.0000.004
reorder_clusters_hclust4.2780.0826.384
reorder_clusters_manual2.2010.0413.551
reorder_clusters_stepdown4.2730.0756.409
reverse_clusters4.5540.0966.741
safeBrew0.0450.0060.078
split_cluster3.9080.0895.691
ssvConsensusIntervalSets0.6760.0311.016
ssvFactorizeMembTable0.0260.0080.044
ssvFeatureBars2.3020.0513.352
ssvFeatureBinaryHeatmap 8.338 1.10114.357
ssvFeatureEuler1.2420.0431.872
ssvFeaturePie2.0800.0873.175
ssvFeatureUpset6.2910.1359.326
ssvFeatureVenn1.5720.0352.378
ssvFetchBam15.080 0.79923.028
ssvFetchBamPE4.5280.4917.317
ssvFetchBigwig3.1790.0754.659
ssvFetchGRanges1.7320.0322.480
ssvFetchSignal3.5180.1325.225
ssvMakeMembTable-methods1.1440.0421.842
ssvOverlapIntervalSets0.5190.0240.762
ssvSignalBandedQuantiles11.453 0.25717.067
ssvSignalClustering4.6770.1297.086
ssvSignalHeatmap.ClusterBars6.7920.1729.549
ssvSignalHeatmap 7.956 0.17511.249
ssvSignalLineplot5.5890.1138.011
ssvSignalLineplotAgg2.4780.0503.613
ssvSignalScatterplot2.8420.0874.439
viewGRangesWinSample_dt2.9350.1284.936
viewGRangesWinSummary_dt2.7470.1373.966
within_clust_sort3.2550.0954.939