Multiple platform build/check report for BioC 3.14 - CHECK results for GenomicDistributions 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: GenomicDistributions

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDistributions.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicDistributions_1.2.0.tar.gz

StartedAt: 2022-04-12 20:13:45 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:21:27 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 462.0 seconds

RetCode: 0

Status: OK

CheckDir: GenomicDistributions.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDistributions.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicDistributions_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicDistributions.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 'GenomicDistributions/DESCRIPTION' ... OK
* this is package 'GenomicDistributions' version '1.2.0'
* 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 'GenomicDistributions' 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getGeneModelsFromGTF   20.03   1.19   36.11
getTssFromGTF          11.89   0.08   11.97
getChromSizesFromFasta  3.08   0.47   55.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getGeneModelsFromGTF   20.11   0.63   28.40
getTssFromGTF          10.72   0.16   10.88
getChromSizesFromFasta  2.83   0.48   27.32
* 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: OK

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenomicDistributions_1.2.0.tar.gz && rm -rf GenomicDistributions.buildbin-libdir && mkdir GenomicDistributions.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicDistributions.buildbin-libdir GenomicDistributions_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenomicDistributions_1.2.0.zip && rm GenomicDistributions_1.2.0.tar.gz GenomicDistributions_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 3856k    7  276k    0     0   460k      0  0:00:08 --:--:--  0:00:08  460k
 37 3856k   37 1444k    0     0   914k      0  0:00:04  0:00:01  0:00:03  913k
 91 3856k   91 3512k    0     0  1361k      0  0:00:02  0:00:02 --:--:-- 1361k
100 3856k  100 3856k    0     0  1427k      0  0:00:02  0:00:02 --:--:-- 1427k

install for i386

* installing *source* package 'GenomicDistributions' ...
** 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 'GenomicDistributions'
    finding HTML links ... done
    BSdtToGRanges                           html  
    GenomicDistributions                    html  
    TSS_hg19                                html  
    binBSGenome                             html  
    binChroms                               html  
    binRegion                               html  
    calcChromBins                           html  
    calcChromBinsRef                        html  
    calcCumulativePartitions                html  
    calcCumulativePartitionsRef             html  
    calcDinuclFreq                          html  
    calcDinuclFreqRef                       html  
    calcExpectedPartitions                  html  
    calcExpectedPartitionsRef               html  
    calcFeatureDist                         html  
    calcFeatureDistRefTSS                   html  
    calcGCContent                           html  
    calcGCContentRef                        html  
    calcNeighborDist                        html  
    calcOpenSignal                          html  
    calcPartitions                          html  
    calcPartitionsRef                       html  
    calcWidth                               html  
    cellTypeMetadata                        html  
    chromSizes_hg19                         html  
    dot-requireAndReturn                    html  
    dot-validateInputs                      html  
    dtToGr                                  html  
    dtToGrInternal                          html  
    exampleOpenSignalMatrix_hg19            html  
    geneModels_hg19                         html  
    genomePartitionList                     html  
    getChromSizes                           html  
    getChromSizesFromFasta                  html  
    getGeneModels                           html  
    getGeneModelsFromGTF                    html  
    getGenomeBins                           html  
    getReferenceData                        html  
    getTssFromGTF                           html  
    grToDt                                  html  
    labelCuts                               html  
    loadBSgenome                            html  
    loadEnsDb                               html  
    neighbordt                              html  
    nlist                                   html  
    plotChromBins                           html  
    plotCumulativePartitions                html  
    plotDinuclFreq                          html  
    plotExpectedPartitions                  html  
    plotFeatureDist                         html  
    plotGCContent                           html  
    plotNeighborDist                        html  
    plotOpenSignal                          html  
    plotPartitions                          html  
    plotQTHist                              html  
    retrieveFile                            html  
    setB_100                                html  
    splitDataTable                          html  
    theme_blank_facet_label                 html  
    vistaEnhancers                          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 'GenomicDistributions' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDistributions' as GenomicDistributions_1.2.0.zip
* DONE (GenomicDistributions)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenomicDistributions' 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.

> library(testthat)
> library("GenomicDistributions")
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> 
> test_check("GenomicDistributions")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]
> 
> proc.time()
   user  system elapsed 
  35.18    1.57   36.76


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.

> library(testthat)
> library("GenomicDistributions")
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> 
> test_check("GenomicDistributions")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]
> 
> proc.time()
   user  system elapsed 
  36.23    0.87   37.09

name	user	system	elapsed
binBSGenome	0	0	0
binChroms	0.02	0.00	0.02
binRegion	0	0	0
calcChromBins	2.51	0.03	2.55
calcChromBinsRef	2.17	0.00	2.17
calcCumulativePartitions	2.58	0.09	2.67
calcCumulativePartitionsRef	2.11	0.11	2.22
calcDinuclFreq	0	0	0
calcDinuclFreqRef	0	0	0
calcExpectedPartitions	1.89	0.08	1.97
calcExpectedPartitionsRef	1.66	0.05	1.70
calcFeatureDist	0.11	0.00	0.11
calcFeatureDistRefTSS	0.18	0.00	0.19
calcGCContent	0	0	0
calcGCContentRef	0	0	0
calcNeighborDist	0.04	0.00	0.03
calcOpenSignal	0.02	0.00	0.02
calcPartitions	1.90	0.00	1.91
calcPartitionsRef	1.43	0.08	1.50
calcWidth	0.43	0.03	0.46
dot-validateInputs	0	0	0
dtToGr	0.02	0.00	0.02
genomePartitionList	1.97	0.03	2.00
getChromSizes	0.02	0.00	0.01
getChromSizesFromFasta	3.08	0.47	55.89
getGeneModels	0.11	0.00	0.11
getGeneModelsFromGTF	20.03	1.19	36.11
getGenomeBins	1.84	0.21	2.06
getTssFromGTF	11.89	0.08	11.97
loadBSgenome	0	0	0
loadEnsDb	0	0	0
nlist	0	0	0
plotChromBins	0.02	0.00	0.02
plotCumulativePartitions	2.37	0.13	2.50
plotDinuclFreq	0.02	0.00	0.01
plotExpectedPartitions	1.78	0.12	1.91
plotFeatureDist	0.19	0.00	0.19
plotGCContent	0.03	0.00	0.03
plotNeighborDist	0	0	0
plotOpenSignal	0.08	0.00	0.08
plotPartitions	1.95	0.06	2.01
plotQTHist	0.36	0.00	0.36
retrieveFile	0	0	0

name	user	system	elapsed
binBSGenome	0	0	0
binChroms	0	0	0
binRegion	0	0	0
calcChromBins	2.84	0.02	2.86
calcChromBinsRef	2.52	0.00	2.52
calcCumulativePartitions	2.86	0.09	2.95
calcCumulativePartitionsRef	2.45	0.08	2.53
calcDinuclFreq	0	0	0
calcDinuclFreqRef	0	0	0
calcExpectedPartitions	1.72	0.09	1.81
calcExpectedPartitionsRef	2.10	0.03	2.13
calcFeatureDist	0.10	0.00	0.11
calcFeatureDistRefTSS	0.18	0.00	0.17
calcGCContent	0	0	0
calcGCContentRef	0	0	0
calcNeighborDist	0.03	0.00	0.04
calcOpenSignal	0.03	0.00	0.03
calcPartitions	1.69	0.04	1.73
calcPartitionsRef	1.68	0.02	1.70
calcWidth	0.54	0.03	0.57
dot-validateInputs	0	0	0
dtToGr	0.03	0.00	0.03
genomePartitionList	2.26	0.05	2.31
getChromSizes	0	0	0
getChromSizesFromFasta	2.83	0.48	27.32
getGeneModels	0.16	0.00	0.16
getGeneModelsFromGTF	20.11	0.63	28.40
getGenomeBins	2.29	0.03	2.33
getTssFromGTF	10.72	0.16	10.88
loadBSgenome	0	0	0
loadEnsDb	0	0	0
nlist	0	0	0
plotChromBins	0.02	0.00	0.01
plotCumulativePartitions	2.23	0.01	2.25
plotDinuclFreq	0.02	0.00	0.02
plotExpectedPartitions	2.44	0.13	2.56
plotFeatureDist	0.2	0.0	0.2
plotGCContent	0.02	0.00	0.01
plotNeighborDist	0.02	0.00	0.02
plotOpenSignal	0.06	0.01	0.08
plotPartitions	1.61	0.11	1.72
plotQTHist	0.34	0.00	0.34
retrieveFile	0	0	0

CHECK results for GenomicDistributions on tokay2

Summary

Command output

Installation output

Tests output

Example timings