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CHECK report for bsseq on tokay1

This page was generated on 2018-04-12 13:21:55 -0400 (Thu, 12 Apr 2018).

Package 163/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.14.0
Kasper Daniel Hansen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/bsseq
Branch: RELEASE_3_6
Last Commit: 9efd7a9
Last Changed Date: 2017-10-30 12:39:45 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bsseq
Version: 1.14.0
Command: rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.14.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.14.0.tar.gz
StartedAt: 2018-04-11 22:37:35 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:44:31 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 416.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: bsseq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.14.0.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.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 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.14.0'
* 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 'bsseq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq-class.Rd:137: missing file link 'setRealizationBackend'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq.Rd:34: missing file link 'DelayedMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqStat-class.Rd:27: missing file link 'DelayedMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqTstat-class.Rd:27: missing file link 'DelayedMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/fisherTests.Rd:55: missing file link 'mclapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/read.bismark.Rd:37: missing file link 'setRealizationBackend'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.8Mb
* 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
Namespace in Imports field not imported from: 'HDF5Array'
  All declared Imports should be used.
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
BSmooth.tstat 10.64   1.36   13.16
getMeth        4.10   0.97    5.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
BSmooth.tstat 8.44   1.33    9.76
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/bsseq.Rcheck/00check.log'
for details.



Installation output

bsseq.Rcheck/00install.out


install for i386

* installing *source* package 'bsseq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'bsseq'
    finding HTML links ... done
    BS.chr22                                html  
    BSmooth                                 html  
    BSmooth.fstat                           html  
    BSmooth.tstat                           html  
    BSseq-class                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq-class.Rd:137: missing file link 'setRealizationBackend'
    BSseq                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseq.Rd:34: missing file link 'DelayedMatrix'
    BSseqStat-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqStat-class.Rd:27: missing file link 'DelayedMatrix'
    BSseqTstat-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/BSseqTstat-class.Rd:27: missing file link 'DelayedMatrix'
    computeStat                             html  
    data.frame2GRanges                      html  
    dmrFinder                               html  
    fisherTests                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/fisherTests.Rd:55: missing file link 'mclapply'
    getCoverage                             html  
    getMeth                                 html  
    getStats                                html  
    goodnessOfFit                           html  
    hasGRanges-class                        html  
    internals                               html  
    plotRegion                              html  
    read.bismark                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCeK7Ut/R.INSTALL1b0c10ef349/bsseq/man/read.bismark.Rd:37: missing file link 'setRealizationBackend'
    read.bsmooth                            html  
    read.umtab                              html  
    smoothSds                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'bsseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.14.0.zip
* DONE (bsseq)
In R CMD INSTALL
In R CMD INSTALL

Tests output

bsseq.Rcheck/tests_i386/runTests.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.

> require("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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: GenomicRanges
Loading required package: stats4
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: 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


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

[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5


RUNIT TEST PROTOCOL -- Wed Apr 11 22:43:42 2018 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bsseq RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  27.65    1.12   45.56 

bsseq.Rcheck/tests_x64/runTests.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.

> require("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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: GenomicRanges
Loading required package: stats4
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: 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


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

[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5


RUNIT TEST PROTOCOL -- Wed Apr 11 22:44:27 2018 
*********************************************** 
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bsseq RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  37.75    1.03   44.42 

Example timings

bsseq.Rcheck/examples_i386/bsseq-Ex.timings

nameusersystemelapsed
BS.chr221.390.071.46
BSmooth000
BSmooth.fstat000
BSmooth.tstat10.64 1.3613.16
BSseq-class2.390.072.53
BSseq1.110.071.17
computeStat000
data.frame2GRanges0.010.000.02
dmrFinder1.660.262.18
fisherTests0.390.020.41
getCoverage2.610.563.17
getMeth4.100.975.06
getStats0.430.090.53
goodnessOfFit3.290.854.42
hasGRanges-class000
read.bismark1.380.113.23
read.umtab000
smoothSds000

bsseq.Rcheck/examples_x64/bsseq-Ex.timings

nameusersystemelapsed
BS.chr221.290.031.33
BSmooth000
BSmooth.fstat000
BSmooth.tstat8.441.339.76
BSseq-class1.970.062.13
BSseq0.800.030.83
computeStat000
data.frame2GRanges0.010.000.02
dmrFinder1.460.221.67
fisherTests0.500.020.51
getCoverage2.590.563.16
getMeth3.541.164.70
getStats0.360.150.52
goodnessOfFit3.031.054.07
hasGRanges-class0.020.000.02
read.bismark1.410.133.03
read.umtab000
smoothSds000