Joseph R Boyd
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/seqsetvis |
| git_branch: master |
| git_last_commit: 8fd65bf |
| git_last_commit_date: 2021-12-07 13:29:30 -0400 (Tue, 07 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:40 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1779/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqsetvis 1.15.6 (landing page) Joseph R Boyd
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: seqsetvis |
| Version: 1.15.6 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seqsetvis_1.15.6.tar.gz |
| StartedAt: 2022-03-17 20:15:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:22:47 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 412.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqsetvis.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqsetvis.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seqsetvis_1.15.6.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/seqsetvis.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.15.6'
* 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 ... 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 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 4.69 1.28 6.03
* 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: OK
seqsetvis.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL seqsetvis
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (seqsetvis)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'segmenter' is missing or broken
done
seqsetvis.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 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 139.20 3.92 143.46
seqsetvis.Rcheck/seqsetvis-Ex.timings
| name | user | system | elapsed | |
| add_cluster_annotation | 1.73 | 0.13 | 1.86 | |
| append_ynorm | 0.01 | 0.00 | 0.01 | |
| applySpline | 0.29 | 0.08 | 0.38 | |
| assemble_heatmap_cluster_bars | 0.55 | 0.00 | 0.54 | |
| calc_norm_factors | 0.02 | 0.00 | 0.02 | |
| centerAtMax | 0.23 | 0.01 | 0.25 | |
| centerFixedSizeGRanges | 0.08 | 0.03 | 0.11 | |
| centerGRangesAtMax | 0.26 | 0.00 | 0.26 | |
| clusteringKmeans | 0.02 | 0.00 | 0.02 | |
| clusteringKmeansNestedHclust | 0.02 | 0.00 | 0.01 | |
| col2hex | 0 | 0 | 0 | |
| collapse_gr | 0.48 | 0.00 | 0.49 | |
| convert_collapsed_coord | 0.12 | 0.02 | 0.14 | |
| crossCorrByRle | 0.3 | 0.0 | 0.3 | |
| easyLoad_FUN | 0.04 | 0.00 | 0.05 | |
| easyLoad_IDRmerged | 0.04 | 0.00 | 0.03 | |
| easyLoad_bed | 0.09 | 0.00 | 0.09 | |
| easyLoad_broadPeak | 0.03 | 0.00 | 0.03 | |
| easyLoad_narrowPeak | 0.03 | 0.00 | 0.04 | |
| easyLoad_seacr | 0.02 | 0.00 | 0.01 | |
| expandCigar | 0.12 | 0.00 | 0.13 | |
| fragLen_calcStranded | 1.54 | 0.00 | 1.55 | |
| fragLen_fromMacs2Xls | 0 | 0 | 0 | |
| getReadLength | 0.05 | 0.01 | 0.06 | |
| ggellipse | 0.63 | 0.00 | 0.63 | |
| harmonize_seqlengths | 0.12 | 0.02 | 0.14 | |
| make_clustering_matrix | 0.02 | 0.00 | 0.01 | |
| merge_clusters | 3.25 | 0.00 | 3.25 | |
| prepare_fetch_GRanges | 0.01 | 0.00 | 0.02 | |
| prepare_fetch_GRanges_names | 0.07 | 0.00 | 0.06 | |
| prepare_fetch_GRanges_width | 0.01 | 0.00 | 0.02 | |
| quantileGRangesWidth | 0 | 0 | 0 | |
| reorder_clusters_hclust | 1.24 | 0.00 | 1.23 | |
| reorder_clusters_manual | 0.7 | 0.0 | 0.7 | |
| reorder_clusters_stepdown | 1.48 | 0.00 | 1.49 | |
| reverse_clusters | 1.86 | 0.00 | 1.86 | |
| safeBrew | 0.03 | 0.00 | 0.03 | |
| split_cluster | 1.49 | 0.03 | 1.51 | |
| ssvConsensusIntervalSets | 0.5 | 0.0 | 0.5 | |
| ssvFactorizeMembTable | 0.02 | 0.00 | 0.02 | |
| ssvFeatureBars | 0.53 | 0.00 | 0.53 | |
| ssvFeatureBinaryHeatmap | 4.69 | 1.28 | 6.03 | |
| ssvFeatureEuler | 0.42 | 0.00 | 0.42 | |
| ssvFeaturePie | 0.98 | 0.05 | 1.03 | |
| ssvFeatureUpset | 1.99 | 0.01 | 2.00 | |
| ssvFeatureVenn | 0.42 | 0.00 | 0.42 | |
| ssvFetchBam | 0 | 0 | 0 | |
| ssvFetchBamPE | 0 | 0 | 0 | |
| ssvFetchBigwig | 0 | 0 | 0 | |
| ssvFetchGRanges | 0.69 | 0.00 | 0.69 | |
| ssvFetchSignal | 1.14 | 0.00 | 1.14 | |
| ssvMakeMembTable-methods | 0.40 | 0.00 | 0.41 | |
| ssvOverlapIntervalSets | 0.19 | 0.00 | 0.19 | |
| ssvSignalBandedQuantiles | 3.69 | 0.04 | 3.71 | |
| ssvSignalClustering | 1.66 | 0.00 | 1.66 | |
| ssvSignalHeatmap.ClusterBars | 1.09 | 0.00 | 1.09 | |
| ssvSignalHeatmap | 1.14 | 0.00 | 1.14 | |
| ssvSignalLineplot | 1.78 | 0.01 | 1.80 | |
| ssvSignalLineplotAgg | 0.77 | 0.00 | 0.77 | |
| ssvSignalScatterplot | 0.58 | 0.00 | 0.58 | |
| viewGRangesWinSample_dt | 0.75 | 0.00 | 0.75 | |
| viewGRangesWinSummary_dt | 0.73 | 0.00 | 0.73 | |
| within_clust_sort | 0.97 | 0.00 | 0.97 | |