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CHECK report for consensusSeekeR on tokay2

This page was generated on 2019-04-09 12:25:19 -0400 (Tue, 09 Apr 2019).

Package 333/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.11.0
Astrid Deschenes
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/consensusSeekeR
Branch: master
Last Commit: cee0907
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: consensusSeekeR
Version: 1.11.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings consensusSeekeR_1.11.0.tar.gz
StartedAt: 2019-04-09 01:58:52 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:03:57 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 305.1 seconds
RetCode: 0
Status:  OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings consensusSeekeR_1.11.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/consensusSeekeR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.11.0'
* 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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/consensusSeekeR_1.11.0.tar.gz && rm -rf consensusSeekeR.buildbin-libdir && mkdir consensusSeekeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.11.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL consensusSeekeR_1.11.0.zip && rm consensusSeekeR_1.11.0.tar.gz consensusSeekeR_1.11.0.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
100  285k  100  285k    0     0  4789k      0 --:--:-- --:--:-- --:--:-- 5497k

install for i386

* installing *source* package 'consensusSeekeR' ...
** 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_1.11.0.zip
* DONE (consensusSeekeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'consensusSeekeR' successfully unpacked and MD5 sums checked

Tests output

consensusSeekeR.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Tue Apr 09 02:03:35 2019 
*********************************************** 
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 
  15.20    0.62   15.92 

consensusSeekeR.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Tue Apr 09 02:03:51 2019 
*********************************************** 
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 
  14.96    0.39   15.35 

Example timings

consensusSeekeR.Rcheck/examples_i386/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.650.280.94
A549_CTCF_MYJ_Peaks_partial0.250.030.28
A549_CTCF_MYN_NarrowPeaks_partial0.310.020.33
A549_CTCF_MYN_Peaks_partial0.420.030.45
A549_FOSL2_01_NarrowPeaks_partial0.220.050.26
A549_FOSL2_01_Peaks_partial0.290.030.31
A549_FOXA1_01_NarrowPeaks_partial0.280.010.30
A549_FOXA1_01_Peaks_partial0.370.030.41
A549_NR3C1_CFQ_NarrowPeaks_partial0.240.050.28
A549_NR3C1_CFQ_Peaks_partial0.280.030.31
A549_NR3C1_CFR_NarrowPeaks_partial0.260.020.28
A549_NR3C1_CFR_Peaks_partial0.320.030.34
A549_NR3C1_CFS_NarrowPeaks_partial0.560.050.61
A549_NR3C1_CFS_Peaks_partial0.790.010.82
NOrMAL_nucleosome_positions0.580.080.65
NOrMAL_nucleosome_ranges0.600.060.66
NucPosSimulator_nucleosome_positions0.590.070.66
NucPosSimulator_nucleosome_ranges0.590.040.64
PING_nucleosome_positions0.470.050.51
PING_nucleosome_ranges0.390.050.44
findConsensusPeakRegions0.630.000.62
findConsensusPeakRegionsValidation0.060.040.11
readNarrowPeakFile0.090.000.09

consensusSeekeR.Rcheck/examples_x64/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.860.070.94
A549_CTCF_MYJ_Peaks_partial0.430.030.45
A549_CTCF_MYN_NarrowPeaks_partial0.490.040.52
A549_CTCF_MYN_Peaks_partial1.200.061.28
A549_FOSL2_01_NarrowPeaks_partial0.310.030.35
A549_FOSL2_01_Peaks_partial0.420.000.42
A549_FOXA1_01_NarrowPeaks_partial0.420.030.45
A549_FOXA1_01_Peaks_partial0.480.030.51
A549_NR3C1_CFQ_NarrowPeaks_partial0.360.030.39
A549_NR3C1_CFQ_Peaks_partial0.430.030.46
A549_NR3C1_CFR_NarrowPeaks_partial0.250.000.25
A549_NR3C1_CFR_Peaks_partial0.250.000.25
A549_NR3C1_CFS_NarrowPeaks_partial0.640.040.67
A549_NR3C1_CFS_Peaks_partial0.860.010.87
NOrMAL_nucleosome_positions0.450.050.50
NOrMAL_nucleosome_ranges0.590.020.61
NucPosSimulator_nucleosome_positions0.710.060.76
NucPosSimulator_nucleosome_ranges0.750.050.80
PING_nucleosome_positions0.500.030.53
PING_nucleosome_ranges0.340.030.38
findConsensusPeakRegions0.770.050.81
findConsensusPeakRegionsValidation0.100.030.14
readNarrowPeakFile0.110.000.11