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CHECK report for consensusSeekeR on tokay1

This page was generated on 2018-04-12 13:27:09 -0400 (Thu, 12 Apr 2018).

Package 287/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.6.0
Astrid Deschenes
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/consensusSeekeR
Branch: RELEASE_3_6
Last Commit: 3a764ca
Last Changed Date: 2017-10-30 12:41:09 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: consensusSeekeR
Version: 1.6.0
Command: rm -rf consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && mkdir consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.6.0.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.6.0.tar.gz
StartedAt: 2018-04-11 23:10:38 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:16:11 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 332.6 seconds
RetCode: 0
Status:  OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && mkdir consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.6.0.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/consensusSeekeR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.6.0'
* 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 installed files from 'inst/doc' ... 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


install for i386

* installing *source* package 'consensusSeekeR' ...
** R
** data
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'consensusSeekeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'consensusSeekeR' as consensusSeekeR_1.6.0.zip
* DONE (consensusSeekeR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

consensusSeekeR.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid



RUNIT TEST PROTOCOL -- Wed Apr 11 23:15:27 2018 
*********************************************** 
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 
  31.40    0.26   31.65

consensusSeekeR.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid



RUNIT TEST PROTOCOL -- Wed Apr 11 23:16:06 2018 
*********************************************** 
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 
  38.60    0.21   38.82

Example timings

consensusSeekeR.Rcheck/examples_i386/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.510.081.59
A549_CTCF_MYJ_Peaks_partial0.560.020.58
A549_CTCF_MYN_NarrowPeaks_partial0.250.000.25
A549_CTCF_MYN_Peaks_partial0.350.000.36
A549_FOSL2_01_NarrowPeaks_partial0.210.010.22
A549_FOSL2_01_Peaks_partial0.500.020.51
A549_FOXA1_01_NarrowPeaks_partial0.480.020.50
A549_FOXA1_01_Peaks_partial0.660.030.69
A549_NR3C1_CFQ_NarrowPeaks_partial0.400.010.42
A549_NR3C1_CFQ_Peaks_partial0.550.030.58
A549_NR3C1_CFR_NarrowPeaks_partial0.360.030.39
A549_NR3C1_CFR_Peaks_partial0.330.050.38
A549_NR3C1_CFS_NarrowPeaks_partial0.730.020.75
A549_NR3C1_CFS_Peaks_partial0.740.010.75
NOrMAL_nucleosome_positions0.610.030.64
NOrMAL_nucleosome_ranges0.670.040.70
NucPosSimulator_nucleosome_positions0.560.010.58
NucPosSimulator_nucleosome_ranges0.560.060.62
PING_nucleosome_positions0.360.020.38
PING_nucleosome_ranges0.410.050.45
findConsensusPeakRegions0.890.030.92
findConsensusPeakRegionsValidation0.030.010.05
readNarrowPeakFile0.140.000.14

consensusSeekeR.Rcheck/examples_x64/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.820.051.87
A549_CTCF_MYJ_Peaks_partial0.650.010.66
A549_CTCF_MYN_NarrowPeaks_partial0.300.020.32
A549_CTCF_MYN_Peaks_partial0.40.00.4
A549_FOSL2_01_NarrowPeaks_partial0.240.030.27
A549_FOSL2_01_Peaks_partial0.360.000.36
A549_FOXA1_01_NarrowPeaks_partial0.340.020.36
A549_FOXA1_01_Peaks_partial0.470.010.48
A549_NR3C1_CFQ_NarrowPeaks_partial0.260.000.26
A549_NR3C1_CFQ_Peaks_partial0.360.030.39
A549_NR3C1_CFR_NarrowPeaks_partial0.270.020.28
A549_NR3C1_CFR_Peaks_partial0.260.010.28
A549_NR3C1_CFS_NarrowPeaks_partial0.830.020.85
A549_NR3C1_CFS_Peaks_partial0.830.030.86
NOrMAL_nucleosome_positions0.580.020.59
NOrMAL_nucleosome_ranges0.580.010.59
NucPosSimulator_nucleosome_positions0.590.020.61
NucPosSimulator_nucleosome_ranges0.610.010.63
PING_nucleosome_positions0.390.020.40
PING_nucleosome_ranges0.300.030.33
findConsensusPeakRegions0.830.000.83
findConsensusPeakRegionsValidation0.030.030.06
readNarrowPeakFile0.160.000.16