Back to Multiple platform build/check report for BioC 3.10
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for DEWSeq on tokay1

This page was generated on 2020-04-15 12:33:29 -0400 (Wed, 15 Apr 2020).

Package 448/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEWSeq 1.0.6
Hentze bioinformatics team
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/DEWSeq
Branch: RELEASE_3_10
Last Commit: 6866854
Last Changed Date: 2020-04-08 04:17:24 -0400 (Wed, 08 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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: DEWSeq
Version: 1.0.6
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEWSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DEWSeq_1.0.6.tar.gz
StartedAt: 2020-04-15 02:40:15 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:49:07 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 532.3 seconds
RetCode: 0
Status:  OK  
CheckDir: DEWSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEWSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DEWSeq_1.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DEWSeq.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEWSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEWSeq' version '1.0.6'
* package encoding: UTF-8
* 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 'DEWSeq' 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 ... NOTE
Package in Depends field not imported from: 'R.utils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'DESeq2:::checkContrast' 'DESeq2:::cleanContrast' 'DESeq2:::getCoef'
  'DESeq2:::getCoefSE' 'DESeq2:::getNworkers' 'DESeq2:::getPvalue'
  'DESeq2:::getStat' 'DESeq2:::lastCoefName' 'DESeq2:::makeWaldTest'
  'DESeq2:::mleContrast'
  See the note in ?`:::` about the use of this operator.
* 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
Examples with CPU or elapsed time > 5s
                user system elapsed
extractRegions 60.38   0.03   60.43
topWindowStats 17.96   0.03   17.98
resultsDEWSeq  14.61   0.16   14.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
extractRegions 57.87   0.11   58.11
topWindowStats 13.97   0.01   14.00
resultsDEWSeq  10.46   0.10   10.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/DEWSeq.Rcheck/00check.log'
for details.



Installation output

DEWSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DEWSeq_1.0.6.tar.gz && rm -rf DEWSeq.buildbin-libdir && mkdir DEWSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEWSeq.buildbin-libdir DEWSeq_1.0.6.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DEWSeq_1.0.6.zip && rm DEWSeq_1.0.6.tar.gz DEWSeq_1.0.6.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
100 2024k  100 2024k    0     0  32.0M      0 --:--:-- --:--:-- --:--:-- 34.0M

install for i386

* installing *source* package 'DEWSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEWSeq'
    finding HTML links ... done
    DESeqDataSetFromSlidingWindows          html  
    SLBP_K562_w50s20                        html  
    dot-readAnnotation                      html  
    extractRegions                          html  
    resultsDEWSeq                           html  
    finding level-2 HTML links ... done

    slbpDds                                 html  
    slbpRegions                             html  
    slbpVst                                 html  
    slbpWindows                             html  
    toBED                                   html  
    topWindowStats                          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 'DEWSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEWSeq' as DEWSeq_1.0.6.zip
* DONE (DEWSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DEWSeq' successfully unpacked and MD5 sums checked

Tests output

DEWSeq.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library("testthat")
> library("DEWSeq")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.23.0 successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

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

    equals

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.9.2 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> test_check("DEWSeq")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |============================                                          |  41%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |==========================================                            |  59%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |======================================================================| 100%
== testthat results  ===========================================================
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  32.31    0.82   33.14 

DEWSeq.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library("testthat")
> library("DEWSeq")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.23.0 successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

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

    equals

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.9.2 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> test_check("DEWSeq")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |============================                                          |  41%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |==========================================                            |  59%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |======================================================================| 100%
== testthat results  ===========================================================
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  40.93    0.60   42.68 

Example timings

DEWSeq.Rcheck/examples_i386/DEWSeq-Ex.timings

nameusersystemelapsed
DESeqDataSetFromSlidingWindows0.580.030.61
SLBP_K562_w50s200.190.000.19
extractRegions60.38 0.0360.43
resultsDEWSeq14.61 0.1614.77
slbpDds0.310.020.33
slbpRegions0.030.000.03
slbpVst0.080.000.08
slbpWindows0.120.010.14
toBED0.360.100.45
topWindowStats17.96 0.0317.98

DEWSeq.Rcheck/examples_x64/DEWSeq-Ex.timings

nameusersystemelapsed
DESeqDataSetFromSlidingWindows0.550.000.55
SLBP_K562_w50s200.220.010.23
extractRegions57.87 0.1158.11
resultsDEWSeq10.46 0.1010.55
slbpDds0.150.010.17
slbpRegions0.020.000.02
slbpVst0.050.000.04
slbpWindows0.060.000.07
toBED0.170.100.26
topWindowStats13.97 0.0114.00