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CHECK report for consensusSeekeR on tokay1

This page was generated on 2019-04-13 11:26:06 -0400 (Sat, 13 Apr 2019).

Package 321/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.10.0
Astrid Deschenes
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/consensusSeekeR
Branch: RELEASE_3_8
Last Commit: c44b75d
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: consensusSeekeR
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings consensusSeekeR_1.10.0.tar.gz
StartedAt: 2019-04-13 01:28:25 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:33:49 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 323.9 seconds
RetCode: 0
Status:  OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings consensusSeekeR_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/consensusSeekeR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/consensusSeekeR_1.10.0.tar.gz && rm -rf consensusSeekeR.buildbin-libdir && mkdir consensusSeekeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL consensusSeekeR_1.10.0.zip && rm consensusSeekeR_1.10.0.tar.gz consensusSeekeR_1.10.0.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  286k  100  286k    0     0  6945k      0 --:--:-- --:--:-- --:--:-- 7739k

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
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_1.10.0.zip
* DONE (consensusSeekeR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'consensusSeekeR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

consensusSeekeR.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 01:33:29 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 
   9.82    0.73   10.62

consensusSeekeR.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 01:33:44 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 
  13.51    0.26   13.78

Example timings

consensusSeekeR.Rcheck/examples_i386/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.010.251.26
A549_CTCF_MYJ_Peaks_partial0.360.030.40
A549_CTCF_MYN_NarrowPeaks_partial0.360.050.41
A549_CTCF_MYN_Peaks_partial0.360.010.37
A549_FOSL2_01_NarrowPeaks_partial0.220.020.24
A549_FOSL2_01_Peaks_partial0.360.050.40
A549_FOXA1_01_NarrowPeaks_partial0.320.060.39
A549_FOXA1_01_Peaks_partial0.460.020.47
A549_NR3C1_CFQ_NarrowPeaks_partial0.250.000.25
A549_NR3C1_CFQ_Peaks_partial0.480.030.52
A549_NR3C1_CFR_NarrowPeaks_partial0.310.010.33
A549_NR3C1_CFR_Peaks_partial0.330.020.34
A549_NR3C1_CFS_NarrowPeaks_partial1.140.031.17
A549_NR3C1_CFS_Peaks_partial1.110.001.11
NOrMAL_nucleosome_positions0.690.060.75
NOrMAL_nucleosome_ranges0.700.050.75
NucPosSimulator_nucleosome_positions0.720.030.75
NucPosSimulator_nucleosome_ranges0.660.060.72
PING_nucleosome_positions0.440.030.47
PING_nucleosome_ranges0.290.050.34
findConsensusPeakRegions0.520.020.53
findConsensusPeakRegionsValidation0.030.030.07
readNarrowPeakFile0.090.000.14

consensusSeekeR.Rcheck/examples_x64/consensusSeekeR-Ex.timings

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.680.050.72
A549_CTCF_MYJ_Peaks_partial0.280.020.30
A549_CTCF_MYN_NarrowPeaks_partial0.270.010.28
A549_CTCF_MYN_Peaks_partial0.340.020.36
A549_FOSL2_01_NarrowPeaks_partial0.210.010.22
A549_FOSL2_01_Peaks_partial0.290.020.31
A549_FOXA1_01_NarrowPeaks_partial0.320.000.31
A549_FOXA1_01_Peaks_partial0.390.010.41
A549_NR3C1_CFQ_NarrowPeaks_partial0.230.020.25
A549_NR3C1_CFQ_Peaks_partial0.340.030.37
A549_NR3C1_CFR_NarrowPeaks_partial0.250.020.27
A549_NR3C1_CFR_Peaks_partial0.240.010.25
A549_NR3C1_CFS_NarrowPeaks_partial0.840.000.84
A549_NR3C1_CFS_Peaks_partial0.750.030.78
NOrMAL_nucleosome_positions0.490.020.50
NOrMAL_nucleosome_ranges0.610.010.63
NucPosSimulator_nucleosome_positions0.640.000.64
NucPosSimulator_nucleosome_ranges0.450.050.50
PING_nucleosome_positions0.330.020.34
PING_nucleosome_ranges0.310.000.32
findConsensusPeakRegions0.580.030.61
findConsensusPeakRegionsValidation0.050.010.06
readNarrowPeakFile0.070.000.08