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This page was generated on 2022-04-13 12:06:37 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for GenomicDistributions on tokay2


To the developers/maintainers of the GenomicDistributions package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 750/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.2.0  (landing page)
Kristyna Kupkova
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: RELEASE_3_14
git_last_commit: 2a030e7
git_last_commit_date: 2021-10-26 13:06:06 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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


Installation output

GenomicDistributions.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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

Tests output

GenomicDistributions.Rcheck/tests_i386/testthat.Rout


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 

GenomicDistributions.Rcheck/tests_x64/testthat.Rout


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 

Example timings

GenomicDistributions.Rcheck/examples_i386/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.020.000.02
binRegion000
calcChromBins2.510.032.55
calcChromBinsRef2.170.002.17
calcCumulativePartitions2.580.092.67
calcCumulativePartitionsRef2.110.112.22
calcDinuclFreq000
calcDinuclFreqRef000
calcExpectedPartitions1.890.081.97
calcExpectedPartitionsRef1.660.051.70
calcFeatureDist0.110.000.11
calcFeatureDistRefTSS0.180.000.19
calcGCContent000
calcGCContentRef000
calcNeighborDist0.040.000.03
calcOpenSignal0.020.000.02
calcPartitions1.900.001.91
calcPartitionsRef1.430.081.50
calcWidth0.430.030.46
dot-validateInputs000
dtToGr0.020.000.02
genomePartitionList1.970.032.00
getChromSizes0.020.000.01
getChromSizesFromFasta 3.08 0.4755.89
getGeneModels0.110.000.11
getGeneModelsFromGTF20.03 1.1936.11
getGenomeBins1.840.212.06
getTssFromGTF11.89 0.0811.97
loadBSgenome000
loadEnsDb000
nlist000
plotChromBins0.020.000.02
plotCumulativePartitions2.370.132.50
plotDinuclFreq0.020.000.01
plotExpectedPartitions1.780.121.91
plotFeatureDist0.190.000.19
plotGCContent0.030.000.03
plotNeighborDist000
plotOpenSignal0.080.000.08
plotPartitions1.950.062.01
plotQTHist0.360.000.36
retrieveFile000

GenomicDistributions.Rcheck/examples_x64/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms000
binRegion000
calcChromBins2.840.022.86
calcChromBinsRef2.520.002.52
calcCumulativePartitions2.860.092.95
calcCumulativePartitionsRef2.450.082.53
calcDinuclFreq000
calcDinuclFreqRef000
calcExpectedPartitions1.720.091.81
calcExpectedPartitionsRef2.100.032.13
calcFeatureDist0.100.000.11
calcFeatureDistRefTSS0.180.000.17
calcGCContent000
calcGCContentRef000
calcNeighborDist0.030.000.04
calcOpenSignal0.030.000.03
calcPartitions1.690.041.73
calcPartitionsRef1.680.021.70
calcWidth0.540.030.57
dot-validateInputs000
dtToGr0.030.000.03
genomePartitionList2.260.052.31
getChromSizes000
getChromSizesFromFasta 2.83 0.4827.32
getGeneModels0.160.000.16
getGeneModelsFromGTF20.11 0.6328.40
getGenomeBins2.290.032.33
getTssFromGTF10.72 0.1610.88
loadBSgenome000
loadEnsDb000
nlist000
plotChromBins0.020.000.01
plotCumulativePartitions2.230.012.25
plotDinuclFreq0.020.000.02
plotExpectedPartitions2.440.132.56
plotFeatureDist0.20.00.2
plotGCContent0.020.000.01
plotNeighborDist0.020.000.02
plotOpenSignal0.060.010.08
plotPartitions1.610.111.72
plotQTHist0.340.000.34
retrieveFile000