Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:13 -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 BindingSiteFinder on tokay2


To the developers/maintainers of the BindingSiteFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BindingSiteFinder.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 150/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 1.0.0  (landing page)
Mirko Br├╝ggemann
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BindingSiteFinder
git_branch: RELEASE_3_14
git_last_commit: be6256c
git_last_commit_date: 2021-10-26 13:11:23 -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: BindingSiteFinder
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BindingSiteFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BindingSiteFinder_1.0.0.tar.gz
StartedAt: 2022-04-12 16:12:04 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:19:44 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 460.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BindingSiteFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BindingSiteFinder_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BindingSiteFinder.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 'BindingSiteFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BindingSiteFinder' version '1.0.0'
* 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 'BindingSiteFinder' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
rangeCoveragePlot 9.94   0.34   10.28
mergeSummaryPlot  8.84   0.36    9.20
supportRatio      5.75   0.22    5.97
makeBindingSites  5.66   0.17    5.83
supportRatioPlot  5.55   0.20    5.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
rangeCoveragePlot     9.39   0.23    9.69
mergeSummaryPlot      8.38   0.27    8.64
supportRatioPlot      7.02   0.25    7.26
supportRatio          6.00   0.21    6.20
reproducibilityFilter 5.72   0.17    5.89
* 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

BindingSiteFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BindingSiteFinder_1.0.0.tar.gz && rm -rf BindingSiteFinder.buildbin-libdir && mkdir BindingSiteFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BindingSiteFinder.buildbin-libdir BindingSiteFinder_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BindingSiteFinder_1.0.0.zip && rm BindingSiteFinder_1.0.0.tar.gz BindingSiteFinder_1.0.0.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
  2 2032k    2 51087    0     0   261k      0  0:00:07 --:--:--  0:00:07  261k
 48 2032k   48  980k    0     0   848k      0  0:00:02  0:00:01  0:00:01  848k
100 2032k  100 2032k    0     0  1134k      0  0:00:01  0:00:01 --:--:-- 1133k

install for i386

* installing *source* package 'BindingSiteFinder' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BindingSiteFinder'
    finding HTML links ... done
    BSFDataSet                              html  
    annotateWithScore                       html  
    coverageOverRanges                      html  
    getMeta                                 html  
    getRanges                               html  
    getSignal                               html  
    getSummary                              html  
    makeBindingSites                        html  
    mergeSummaryPlot                        html  
    rangeCoveragePlot                       html  
    reproducibilityFilter                   html  
    reproducibiliyCutoffPlot                html  
    setRanges                               html  
    setSignal                               html  
    setSummary                              html  
    show                                    html  
    supportRatio                            html  
    supportRatioPlot                        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 'BindingSiteFinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BindingSiteFinder' as BindingSiteFinder_1.0.0.zip
* DONE (BindingSiteFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BindingSiteFinder' successfully unpacked and MD5 sums checked

Tests output

BindingSiteFinder.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("BindingSiteFinder")
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> test_check("BindingSiteFinder")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  40.62    2.32   42.93 

BindingSiteFinder.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("BindingSiteFinder")
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> test_check("BindingSiteFinder")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  40.29    1.35   41.65 

Example timings

BindingSiteFinder.Rcheck/examples_i386/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.350.021.40
annotateWithScore000
coverageOverRanges1.940.112.04
getMeta0.090.000.10
getRanges0.120.000.12
getSignal0.150.000.14
getSummary3.040.503.55
makeBindingSites5.660.175.83
mergeSummaryPlot8.840.369.20
rangeCoveragePlot 9.94 0.3410.28
reproducibilityFilter4.020.204.22
reproducibiliyCutoffPlot4.340.074.41
setRanges0.090.000.09
setSignal0.080.030.11
setSummary0.110.000.11
show0.090.000.09
supportRatio5.750.225.97
supportRatioPlot5.550.205.75

BindingSiteFinder.Rcheck/examples_x64/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.890.000.89
annotateWithScore000
coverageOverRanges2.080.112.19
getMeta0.090.000.10
getRanges0.110.000.11
getSignal0.140.000.14
getSummary3.070.103.17
makeBindingSites4.610.084.69
mergeSummaryPlot8.380.278.64
rangeCoveragePlot9.390.239.69
reproducibilityFilter5.720.175.89
reproducibiliyCutoffPlot3.900.073.97
setRanges0.100.000.09
setSignal0.090.000.10
setSummary0.090.000.09
show0.070.010.08
supportRatio6.000.216.20
supportRatioPlot7.020.257.26