Multiple platform build/check report for BioC 3.14 - CHECK results for seqsetvis on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: seqsetvis

Version: 1.14.4

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqsetvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings seqsetvis_1.14.4.tar.gz

StartedAt: 2022-04-13 02:47:50 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:02:48 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 898.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: seqsetvis.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqsetvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings seqsetvis_1.14.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seqsetvis.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqsetvis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqsetvis' version '1.14.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ... WARNING
Codoc mismatches from documentation object 'harmonize_seqlengths':
harmonize_seqlengths
  Code: function(query_gr, bam_file, force_fix = FALSE)
  Docs: function(gr, bam_file)
  Argument names in code not in docs:
    query_gr force_fix
  Argument names in docs not in code:
    gr
  Mismatches in argument names:
    Position: 1 Code: query_gr Docs: gr

* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ssvSignalBandedQuantiles 6.75   0.23   13.33
ssvSignalClustering      3.02   0.02    9.16
ssvSignalHeatmap         2.78   0.02    9.20
split_cluster            2.46   0.01    6.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ssvSignalBandedQuantiles  8.48   0.07   12.43
ssvSignalLineplot         3.99   0.01    7.08
ssvFetchSignal            3.80   0.06    5.66
reorder_clusters_stepdown 3.75   0.00    6.78
ssvSignalHeatmap          2.09   0.00    5.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/seqsetvis.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/seqsetvis_1.14.4.tar.gz && rm -rf seqsetvis.buildbin-libdir && mkdir seqsetvis.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqsetvis.buildbin-libdir seqsetvis_1.14.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL seqsetvis_1.14.4.zip && rm seqsetvis_1.14.4.tar.gz seqsetvis_1.14.4.zip
###
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100  557k  100  557k    0     0   607k      0 --:--:-- --:--:-- --:--:--  606k
100  557k  100  557k    0     0   606k      0 --:--:-- --:--:-- --:--:--  606k

install for i386

* 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
  converting help for package 'seqsetvis'
    finding HTML links ... done
    Bcell_peaks                             html  
    CTCF_in_10a_bigWig_urls                 html  
    CTCF_in_10a_data                        html  
    CTCF_in_10a_narrowPeak_grs              html  
    CTCF_in_10a_narrowPeak_urls             html  
    CTCF_in_10a_overlaps_gr                 html  
    CTCF_in_10a_profiles_dt                 html  
    CTCF_in_10a_profiles_gr                 html  
    add_cluster_annotation                  html  
    append_ynorm                            html  
    applySpline                             html  
    assemble_heatmap_cluster_bars           html  
    calc_norm_factors                       html  
    centerAtMax                             html  
    centerFixedSizeGRanges                  html  
    centerGRangesAtMax                      html  
    chromHMM_demo_bw_states_gr              html  
    chromHMM_demo_chain_url                 html  
    chromHMM_demo_data                      html  
    chromHMM_demo_overlaps_gr               html  
    chromHMM_demo_segmentation_url          html  
    chromHMM_demo_state_colors              html  
    chromHMM_demo_state_total_widths        html  
    clusteringKmeans                        html  
    clusteringKmeansNestedHclust            html  
    col2hex                                 html  
    collapse_gr                             html  
    convert_collapsed_coord                 html  
    crossCorrByRle                          html  
    dot-expand_cigar_dt                     html  
    dot-expand_cigar_dt_recursive           html  
    dot-rm_dupes                            html  
    dot-rm_dupesPE                          html  
    easyLoad_FUN                            html  
    easyLoad_IDRmerged                      html  
    easyLoad_bed                            html  
    easyLoad_broadPeak                      html  
    easyLoad_narrowPeak                     html  
    easyLoad_seacr                          html  
    expandCigar                             html  
    fetchBam                                html  
    fragLen_calcStranded                    html  
    fragLen_fromMacs2Xls                    html  
    getReadLength                           html  
    ggellipse                               html  
    harmonize_seqlengths                    html  
    make_clustering_matrix                  html  
    merge_clusters                          html  
    prepare_fetch_GRanges                   html  
    prepare_fetch_GRanges_names             html  
    prepare_fetch_GRanges_width             html  
    quantileGRangesWidth                    html  
    reorder_clusters_hclust                 html  
    reorder_clusters_manual                 html  
    reorder_clusters_stepdown               html  
    reverse_clusters                        html  
    safeBrew                                html  
    seqsetvis-package                       html  
    set_list2memb                           html  
    shift_anchor                            html  
    split_cluster                           html  
    ssvConsensusIntervalSets                html  
    ssvFactorizeMembTable                   html  
    ssvFeatureBars                          html  
    ssvFeatureBinaryHeatmap                 html  
    ssvFeatureEuler                         html  
    ssvFeaturePie                           html  
    ssvFeatureUpset                         html  
    ssvFeatureVenn                          html  
    ssvFetchBam                             html  
    ssvFetchBam.single                      html  
    ssvFetchBamPE                           html  
    ssvFetchBamPE.single                    html  
    ssvFetchBigwig                          html  
    ssvFetchBigwig.single                   html  
    ssvFetchGRanges                         html  
    ssvFetchSignal                          html  
    ssvMakeMembTable-methods                html  
    ssvOverlapIntervalSets                  html  
    ssvSignalBandedQuantiles                html  
    ssvSignalClustering                     html  
    ssvSignalHeatmap.ClusterBars            html  
    ssvSignalHeatmap                        html  
    ssvSignalLineplot                       html  
    ssvSignalLineplotAgg                    html  
    ssvSignalScatterplot                    html  
    ssv_mclapply                            html  
    test_peaks                              html  
    viewGRangesWinSample_dt                 html  
    viewGRangesWinSummary_dt                html  
    within_clust_sort                       html  
** 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

install for x64

* installing *source* package 'seqsetvis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqsetvis' as seqsetvis_1.14.4.zip
* DONE (seqsetvis)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'seqsetvis' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 710 ]

== Skipped tests ===============================================================
* On Windows (37)

[ FAIL 0 | WARN 0 | SKIP 37 | PASS 710 ]
> 
> proc.time()
   user  system elapsed 
 196.75    2.84  199.90


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 710 ]

== Skipped tests ===============================================================
* On Windows (37)

[ FAIL 0 | WARN 0 | SKIP 37 | PASS 710 ]
> 
> proc.time()
   user  system elapsed 
 218.76    1.14  220.00

name	user	system	elapsed
add_cluster_annotation	1.03	0.30	1.32
append_ynorm	0.03	0.02	0.05
applySpline	0.55	0.03	0.58
assemble_heatmap_cluster_bars	0.57	0.00	0.57
calc_norm_factors	0	0	0
centerAtMax	0.48	0.03	0.51
centerFixedSizeGRanges	0.16	0.03	0.19
centerGRangesAtMax	0.50	0.05	0.53
clusteringKmeans	0.02	0.00	0.01
clusteringKmeansNestedHclust	0.06	0.00	0.05
col2hex	0	0	0
collapse_gr	1.09	0.00	1.09
convert_collapsed_coord	0.18	0.00	0.19
crossCorrByRle	0.44	0.23	0.67
easyLoad_FUN	0.09	0.03	0.13
easyLoad_IDRmerged	0.21	0.02	0.22
easyLoad_bed	0.19	0.00	0.19
easyLoad_broadPeak	0.06	0.00	0.06
easyLoad_narrowPeak	0.06	0.00	0.06
easyLoad_seacr	0.05	0.00	0.05
expandCigar	0.32	0.01	0.33
fragLen_calcStranded	1.89	0.18	2.06
fragLen_fromMacs2Xls	0	0	0
getReadLength	0.06	0.00	0.07
ggellipse	0.42	0.01	0.43
harmonize_seqlengths	0.09	0.00	0.10
make_clustering_matrix	0.00	0.02	0.01
merge_clusters	2.57	0.12	2.67
prepare_fetch_GRanges	0.04	0.00	0.05
prepare_fetch_GRanges_names	0.14	0.00	0.14
prepare_fetch_GRanges_width	0.05	0.00	0.05
quantileGRangesWidth	0	0	0
reorder_clusters_hclust	1.45	0.00	1.45
reorder_clusters_manual	0.72	0.00	0.72
reorder_clusters_stepdown	1.72	0.03	1.75
reverse_clusters	2.59	0.02	3.65
safeBrew	0.03	0.00	0.03
split_cluster	2.46	0.01	6.13
ssvConsensusIntervalSets	0.81	0.04	1.00
ssvFactorizeMembTable	0.04	0.01	0.06
ssvFeatureBars	0.93	0.05	0.97
ssvFeatureBinaryHeatmap	0.64	0.00	0.64
ssvFeatureEuler	0.68	0.00	0.68
ssvFeaturePie	0.71	0.00	0.71
ssvFeatureUpset	3.31	0.00	4.34
ssvFeatureVenn	0.72	0.02	0.74
ssvFetchBam	0.00	0.00	0.02
ssvFetchBamPE	0	0	0
ssvFetchBigwig	0	0	0
ssvFetchGRanges	1.86	0.00	4.00
ssvFetchSignal	3.10	0.01	3.82
ssvMakeMembTable-methods	0.73	0.02	0.75
ssvOverlapIntervalSets	0.33	0.00	0.33
ssvSignalBandedQuantiles	6.75	0.23	13.33
ssvSignalClustering	3.02	0.02	9.16
ssvSignalHeatmap.ClusterBars	2.45	0.03	2.78
ssvSignalHeatmap	2.78	0.02	9.20
ssvSignalLineplot	3.55	0.00	4.31
ssvSignalLineplotAgg	1.14	0.01	1.16
ssvSignalScatterplot	0.75	0.02	0.76
viewGRangesWinSample_dt	1.53	0.01	1.55
viewGRangesWinSummary_dt	1.36	0.00	1.36
within_clust_sort	1.27	0.02	1.28

name	user	system	elapsed
add_cluster_annotation	1.95	0.01	1.98
append_ynorm	0.05	0.00	0.05
applySpline	0.47	0.05	0.51
assemble_heatmap_cluster_bars	0.56	0.00	0.57
calc_norm_factors	0.02	0.00	0.01
centerAtMax	0.47	0.03	0.50
centerFixedSizeGRanges	0.16	0.03	0.19
centerGRangesAtMax	0.58	0.00	0.58
clusteringKmeans	0.01	0.00	0.02
clusteringKmeansNestedHclust	0.04	0.00	0.03
col2hex	0	0	0
collapse_gr	1.01	0.03	1.05
convert_collapsed_coord	0.24	0.03	0.26
crossCorrByRle	0.54	0.02	0.58
easyLoad_FUN	0.07	0.00	0.06
easyLoad_IDRmerged	0.10	0.00	0.11
easyLoad_bed	0.15	0.00	0.14
easyLoad_broadPeak	0.06	0.00	0.06
easyLoad_narrowPeak	0.06	0.02	0.08
easyLoad_seacr	0.05	0.00	0.05
expandCigar	0.25	0.00	0.25
fragLen_calcStranded	1.84	0.00	1.84
fragLen_fromMacs2Xls	0	0	0
getReadLength	0.06	0.00	0.07
ggellipse	0.49	0.00	0.48
harmonize_seqlengths	0.09	0.01	0.11
make_clustering_matrix	0.02	0.00	0.02
merge_clusters	3.15	0.00	3.15
prepare_fetch_GRanges	0.05	0.00	0.04
prepare_fetch_GRanges_names	0.20	0.00	0.21
prepare_fetch_GRanges_width	0.06	0.00	0.06
quantileGRangesWidth	0.00	0.02	0.02
reorder_clusters_hclust	1.95	0.01	1.96
reorder_clusters_manual	0.93	0.00	0.93
reorder_clusters_stepdown	3.75	0.00	6.78
reverse_clusters	2.64	0.02	2.92
safeBrew	0.04	0.00	0.05
split_cluster	2.33	0.01	4.85
ssvConsensusIntervalSets	0.94	0.02	0.95
ssvFactorizeMembTable	0.03	0.00	0.03
ssvFeatureBars	0.89	0.00	1.41
ssvFeatureBinaryHeatmap	0.75	0.00	0.75
ssvFeatureEuler	0.78	0.02	0.93
ssvFeaturePie	1.00	0.00	1.18
ssvFeatureUpset	3.40	0.00	4.21
ssvFeatureVenn	0.47	0.00	0.47
ssvFetchBam	0	0	0
ssvFetchBamPE	0	0	0
ssvFetchBigwig	0	0	0
ssvFetchGRanges	2.05	0.00	2.39
ssvFetchSignal	3.80	0.06	5.66
ssvMakeMembTable-methods	1.26	0.00	1.27
ssvOverlapIntervalSets	0.32	0.01	0.32
ssvSignalBandedQuantiles	8.48	0.07	12.43
ssvSignalClustering	2.00	0.00	2.48
ssvSignalHeatmap.ClusterBars	1.44	0.00	1.42
ssvSignalHeatmap	2.09	0.00	5.52
ssvSignalLineplot	3.99	0.01	7.08
ssvSignalLineplotAgg	1.37	0.00	2.60
ssvSignalScatterplot	0.94	0.00	0.94
viewGRangesWinSample_dt	1.87	0.00	1.88
viewGRangesWinSummary_dt	1.24	0.00	1.23
within_clust_sort	1.06	0.00	1.06

CHECK results for seqsetvis on tokay2

Summary

Command output

Installation output

Tests output

Example timings