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This page was generated on 2021-09-22 15:05:11 -0400 (Wed, 22 Sep 2021).

CHECK results for consensusSeekeR on tokay2

To the developers/maintainers of the consensusSeekeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consensusSeekeR.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.

raw results

Package 381/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.20.0  (landing page)
Astrid Deschenes
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/consensusSeekeR
git_branch: RELEASE_3_13
git_last_commit: e7f757a
git_last_commit_date: 2021-05-19 12:16:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: consensusSeekeR
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings consensusSeekeR_1.20.0.tar.gz
StartedAt: 2021-09-21 21:12:22 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 21:17:27 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 304.4 seconds
RetCode: 0
Status:   OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings consensusSeekeR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/consensusSeekeR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'consensusSeekeR/DESCRIPTION' ... OK
* this is package 'consensusSeekeR' version '1.20.0'
* 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 'consensusSeekeR' 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

consensusSeekeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/consensusSeekeR_1.20.0.tar.gz && rm -rf consensusSeekeR.buildbin-libdir && mkdir consensusSeekeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL consensusSeekeR_1.20.0.zip && rm consensusSeekeR_1.20.0.tar.gz consensusSeekeR_1.20.0.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
 76  285k   76  217k    0     0   947k      0 --:--:-- --:--:-- --:--:--  945k
100  285k  100  285k    0     0  1070k      0 --:--:-- --:--:-- --:--:-- 1070k

install for i386

* installing *source* package 'consensusSeekeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'consensusSeekeR'
    finding HTML links ... done
    A549_CTCF_MYJ_NarrowPeaks_partial       html  
    A549_CTCF_MYJ_Peaks_partial             html  
    A549_CTCF_MYN_NarrowPeaks_partial       html  
    A549_CTCF_MYN_Peaks_partial             html  
    A549_FOSL2_01_NarrowPeaks_partial       html  
    A549_FOSL2_01_Peaks_partial             html  
    A549_FOXA1_01_NarrowPeaks_partial       html  
    A549_FOXA1_01_Peaks_partial             html  
    A549_NR3C1_CFQ_NarrowPeaks_partial      html  
    A549_NR3C1_CFQ_Peaks_partial            html  
    A549_NR3C1_CFR_NarrowPeaks_partial      html  
    A549_NR3C1_CFR_Peaks_partial            html  
    A549_NR3C1_CFS_NarrowPeaks_partial      html  
    A549_NR3C1_CFS_Peaks_partial            html  
    NOrMAL_nucleosome_positions             html  
    NOrMAL_nucleosome_ranges                html  
    NucPosSimulator_nucleosome_positions    html  
    NucPosSimulator_nucleosome_ranges       html  
    PING_nucleosome_positions               html  
    PING_nucleosome_ranges                  html  
    consensusSeekeR-package                 html  
    findConsensusPeakRegions                html  
    findConsensusPeakRegionsForOneChrom     html  
    findConsensusPeakRegionsValidation      html  
    isInteger                               html  
    readNarrowPeakFile                      html  
    refineRegion                            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 'consensusSeekeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'consensusSeekeR' as consensusSeekeR_1.20.0.zip
* DONE (consensusSeekeR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'consensusSeekeR' successfully unpacked and MD5 sums checked

Tests output

consensusSeekeR.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> ## Run all tests present in the package
> BiocGenerics:::testPackage("consensusSeekeR")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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


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



RUNIT TEST PROTOCOL -- Tue Sep 21 21:17:03 2021 
*********************************************** 
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensusSeekeR RUnit Tests - 56 test functions, 0 errors, 0 failures
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  14.56    0.90   15.54 

consensusSeekeR.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> ## Run all tests present in the package
> BiocGenerics:::testPackage("consensusSeekeR")

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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


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



RUNIT TEST PROTOCOL -- Tue Sep 21 21:17:19 2021 
*********************************************** 
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
consensusSeekeR RUnit Tests - 56 test functions, 0 errors, 0 failures
Number of test functions: 56 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.37    0.40   15.78 

Example timings

consensusSeekeR.Rcheck/examples_i386/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.560.071.64
A549_CTCF_MYJ_Peaks_partial0.500.020.52
A549_CTCF_MYN_NarrowPeaks_partial0.440.030.47
A549_CTCF_MYN_Peaks_partial0.460.100.56
A549_FOSL2_01_NarrowPeaks_partial0.380.010.39
A549_FOSL2_01_Peaks_partial0.510.020.53
A549_FOXA1_01_NarrowPeaks_partial0.490.010.50
A549_FOXA1_01_Peaks_partial0.640.030.67
A549_NR3C1_CFQ_NarrowPeaks_partial0.410.000.41
A549_NR3C1_CFQ_Peaks_partial0.500.030.53
A549_NR3C1_CFR_NarrowPeaks_partial0.390.040.42
A549_NR3C1_CFR_Peaks_partial0.390.010.41
A549_NR3C1_CFS_NarrowPeaks_partial1.280.191.47
A549_NR3C1_CFS_Peaks_partial1.280.011.29
NOrMAL_nucleosome_positions0.870.040.91
NOrMAL_nucleosome_ranges0.900.040.94
NucPosSimulator_nucleosome_positions0.810.030.84
NucPosSimulator_nucleosome_ranges0.840.020.86
PING_nucleosome_positions0.500.030.53
PING_nucleosome_ranges0.390.050.44
findConsensusPeakRegions0.970.010.98
findConsensusPeakRegionsValidation0.090.000.10
readNarrowPeakFile0.110.000.11

consensusSeekeR.Rcheck/examples_x64/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.880.110.99
A549_CTCF_MYJ_Peaks_partial0.430.020.45
A549_CTCF_MYN_NarrowPeaks_partial0.410.010.42
A549_CTCF_MYN_Peaks_partial0.510.020.53
A549_FOSL2_01_NarrowPeaks_partial0.420.010.44
A549_FOSL2_01_Peaks_partial0.570.000.56
A549_FOXA1_01_NarrowPeaks_partial0.510.020.53
A549_FOXA1_01_Peaks_partial0.720.020.74
A549_NR3C1_CFQ_NarrowPeaks_partial0.580.010.59
A549_NR3C1_CFQ_Peaks_partial0.720.050.76
A549_NR3C1_CFR_NarrowPeaks_partial0.450.010.47
A549_NR3C1_CFR_Peaks_partial0.450.000.46
A549_NR3C1_CFS_NarrowPeaks_partial0.940.030.97
A549_NR3C1_CFS_Peaks_partial0.950.000.95
NOrMAL_nucleosome_positions0.890.020.90
NOrMAL_nucleosome_ranges0.910.030.94
NucPosSimulator_nucleosome_positions0.860.050.91
NucPosSimulator_nucleosome_ranges0.880.010.89
PING_nucleosome_positions0.530.020.55
PING_nucleosome_ranges0.420.030.45
findConsensusPeakRegions0.970.031.00
findConsensusPeakRegionsValidation0.090.020.11
readNarrowPeakFile0.090.000.09