Multiple platform build/check report for BioC 3.7 - CHECK report for consensusSeekeR on tokay2

Package: consensusSeekeR

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings consensusSeekeR_1.8.0.tar.gz

StartedAt: 2018-10-17 01:19:05 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:23:41 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 276.0 seconds

RetCode: 0

Status: OK

CheckDir: consensusSeekeR.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:consensusSeekeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings consensusSeekeR_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/consensusSeekeR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.8.0'
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/consensusSeekeR_1.8.0.tar.gz && rm -rf consensusSeekeR.buildbin-libdir && mkdir consensusSeekeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL consensusSeekeR_1.8.0.zip && rm consensusSeekeR_1.8.0.tar.gz consensusSeekeR_1.8.0.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  4527k      0 --:--:-- --:--:-- --:--:-- 5015k

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_1.8.0.zip
* DONE (consensusSeekeR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'consensusSeekeR' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, 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 -- Wed Oct 17 01:23:21 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 
  11.79    0.95   13.09


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, 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 -- Wed Oct 17 01:23:36 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 
  13.50    0.34   13.82

name	user	system	elapsed
A549_CTCF_MYJ_NarrowPeaks_partial	0.73	0.23	0.97
A549_CTCF_MYJ_Peaks_partial	0.35	0.02	0.36
A549_CTCF_MYN_NarrowPeaks_partial	0.28	0.03	0.31
A549_CTCF_MYN_Peaks_partial	0.36	0.03	0.39
A549_FOSL2_01_NarrowPeaks_partial	0.23	0.03	0.26
A549_FOSL2_01_Peaks_partial	0.31	0.02	0.33
A549_FOXA1_01_NarrowPeaks_partial	0.33	0.01	0.34
A549_FOXA1_01_Peaks_partial	0.42	0.02	0.44
A549_NR3C1_CFQ_NarrowPeaks_partial	0.32	0.01	0.33
A549_NR3C1_CFQ_Peaks_partial	0.32	0.05	0.38
A549_NR3C1_CFR_NarrowPeaks_partial	0.25	0.02	0.26
A549_NR3C1_CFR_Peaks_partial	0.24	0.01	0.25
A549_NR3C1_CFS_NarrowPeaks_partial	0.72	0.00	0.72
A549_NR3C1_CFS_Peaks_partial	0.67	0.00	0.67
NOrMAL_nucleosome_positions	0.50	0.02	0.51
NOrMAL_nucleosome_ranges	0.43	0.05	0.49
NucPosSimulator_nucleosome_positions	0.53	0.04	0.58
NucPosSimulator_nucleosome_ranges	0.54	0.03	0.56
PING_nucleosome_positions	0.29	0.05	0.34
PING_nucleosome_ranges	0.25	0.05	0.30
findConsensusPeakRegions	0.60	0.01	0.61
findConsensusPeakRegionsValidation	0.06	0.05	0.11
readNarrowPeakFile	0.16	0.00	0.19

name	user	system	elapsed
A549_CTCF_MYJ_NarrowPeaks_partial	0.70	0.11	0.82
A549_CTCF_MYJ_Peaks_partial	0.47	0.04	0.51
A549_CTCF_MYN_NarrowPeaks_partial	0.29	0.03	0.33
A549_CTCF_MYN_Peaks_partial	0.38	0.02	0.39
A549_FOSL2_01_NarrowPeaks_partial	0.41	0.03	0.43
A549_FOSL2_01_Peaks_partial	0.42	0.02	0.44
A549_FOXA1_01_NarrowPeaks_partial	0.31	0.03	0.35
A549_FOXA1_01_Peaks_partial	0.55	0.01	0.56
A549_NR3C1_CFQ_NarrowPeaks_partial	0.42	0.03	0.45
A549_NR3C1_CFQ_Peaks_partial	0.44	0.07	0.50
A549_NR3C1_CFR_NarrowPeaks_partial	0.28	0.01	0.30
A549_NR3C1_CFR_Peaks_partial	0.28	0.02	0.30
A549_NR3C1_CFS_NarrowPeaks_partial	1.00	0.01	1.01
A549_NR3C1_CFS_Peaks_partial	0.90	0.02	0.92
NOrMAL_nucleosome_positions	0.80	0.03	0.83
NOrMAL_nucleosome_ranges	0.78	0.06	0.84
NucPosSimulator_nucleosome_positions	0.78	0.03	0.82
NucPosSimulator_nucleosome_ranges	0.66	0.04	0.68
PING_nucleosome_positions	0.36	0.03	0.40
PING_nucleosome_ranges	0.30	0.01	0.31
findConsensusPeakRegions	0.78	0.02	0.79
findConsensusPeakRegionsValidation	0.06	0.01	0.08
readNarrowPeakFile	0.06	0.00	0.07

CHECK report for consensusSeekeR on tokay2

Summary

Command output

Installation output

Tests output

Example timings