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CHECK report for BUMHMM on tokay1

This page was generated on 2018-04-12 13:29:07 -0400 (Thu, 12 Apr 2018).

Package 167/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUMHMM 1.2.0
Alina Selega
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BUMHMM
Branch: RELEASE_3_6
Last Commit: cfda7a4
Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BUMHMM
Version: 1.2.0
Command: rm -rf BUMHMM.buildbin-libdir BUMHMM.Rcheck && mkdir BUMHMM.buildbin-libdir BUMHMM.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BUMHMM.buildbin-libdir BUMHMM_1.2.0.tar.gz >BUMHMM.Rcheck\00install.out 2>&1 && cp BUMHMM.Rcheck\00install.out BUMHMM-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BUMHMM.buildbin-libdir --install="check:BUMHMM-install.out" --force-multiarch --no-vignettes --timings BUMHMM_1.2.0.tar.gz
StartedAt: 2018-04-11 22:38:03 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:41:43 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 220.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BUMHMM.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BUMHMM.buildbin-libdir BUMHMM.Rcheck && mkdir BUMHMM.buildbin-libdir BUMHMM.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BUMHMM.buildbin-libdir BUMHMM_1.2.0.tar.gz >BUMHMM.Rcheck\00install.out 2>&1 && cp BUMHMM.Rcheck\00install.out BUMHMM-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BUMHMM.buildbin-libdir --install="check:BUMHMM-install.out" --force-multiarch --no-vignettes --timings BUMHMM_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BUMHMM.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 'BUMHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUMHMM' version '1.2.0'
* 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 'BUMHMM' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/findPatternPos.Rd:33: missing file link 'stri_locate_all_fixed'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/nuclPerm.Rd:19: missing file link 'permutations'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/nuclPerm.Rd:40: missing file link 'permutations'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BUMHMM.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 '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 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BUMHMM.Rcheck/00check.log'
for details.

Installation output

BUMHMM.Rcheck/00install.out


install for i386

* installing *source* package 'BUMHMM' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BUMHMM'
    finding HTML links ... done
    computeProbs                            html  
    finding level-2 HTML links ... done

    computeStretches                        html  
    covFile                                 html  
    docFile                                 html  
    dorFile                                 html  
    findPatternPos                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/findPatternPos.Rd:33: missing file link 'stri_locate_all_fixed'
    nuclPerm                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/nuclPerm.Rd:19: missing file link 'permutations'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwrH3gV/R.INSTALL258015d67d13/BUMHMM/man/nuclPerm.Rd:40: missing file link 'permutations'
    scaleDOR                                html  
    se                                      html  
    selectNuclPos                           html  
    seq                                     html  
    stabiliseVariance                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BUMHMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUMHMM' as BUMHMM_1.2.0.zip
* DONE (BUMHMM)
In R CMD INSTALL
In R CMD INSTALL

Tests output

BUMHMM.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(BUMHMM)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
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, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

> library(Biostrings)
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

> 
> test_check("BUMHMM")
== testthat results  ===========================================================
OK: 42 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.85    0.18    6.03

BUMHMM.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(BUMHMM)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
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, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

> library(Biostrings)
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

> 
> test_check("BUMHMM")
== testthat results  ===========================================================
OK: 42 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.40    0.14    7.53

Example timings

BUMHMM.Rcheck/examples_i386/BUMHMM-Ex.timings

nameusersystemelapsed
computeProbs1.320.091.41
computeStretches0.020.000.02
findPatternPos0.140.000.14
nuclPerm0.050.000.05
scaleDOR0.000.020.02
selectNuclPos0.020.030.04
stabiliseVariance0.590.060.66

BUMHMM.Rcheck/examples_x64/BUMHMM-Ex.timings

nameusersystemelapsed
computeProbs1.660.031.69
computeStretches0.030.000.03
findPatternPos0.160.020.17
nuclPerm0.050.000.05
scaleDOR0.010.000.01
selectNuclPos0.000.030.03
stabiliseVariance0.810.010.83