Package: segmentSeq

Version: 2.12.0

Command: rm -rf segmentSeq.buildbin-libdir segmentSeq.Rcheck && mkdir segmentSeq.buildbin-libdir segmentSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_2.12.0.tar.gz >segmentSeq.Rcheck\00install.out 2>&1 && cp segmentSeq.Rcheck\00install.out segmentSeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_2.12.0.tar.gz

StartedAt: 2018-04-12 03:02:45 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:11:03 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 497.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: segmentSeq.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf segmentSeq.buildbin-libdir segmentSeq.Rcheck && mkdir segmentSeq.buildbin-libdir segmentSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=segmentSeq.buildbin-libdir segmentSeq_2.12.0.tar.gz >segmentSeq.Rcheck\00install.out 2>&1 && cp segmentSeq.Rcheck\00install.out segmentSeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=segmentSeq.buildbin-libdir --install="check:segmentSeq-install.out" --force-multiarch --no-vignettes --timings segmentSeq_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/segmentSeq.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 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.12.0'
* 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 'segmentSeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/classifySeg.Rd:45: missing file link 'getPriors.NB'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/lociLikelihoods.Rd:27: missing file link 'getLikelihoods.NB'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segClass-class.Rd:23: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segData-class.Rd:25: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segMeth-class.Rd:25: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/segmentSeq.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 ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
  'sDP'
Undefined global functions or variables:
  sDP
* 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
classifySeg     21.08   0.06   21.14
heuristicSeg     8.87   0.00    8.88
normaliseNC      8.19   0.42    8.61
lociLikelihoods  8.36   0.00    8.36
thresholdFinder  6.12   0.39    6.52
readMeths        5.15   0.29    5.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classifySeg     36.86   0.01   36.87
heuristicSeg    14.61   0.02   14.63
lociLikelihoods 13.62   0.00   13.63
normaliseNC      9.04   0.58    9.61
thresholdFinder  5.91   0.61    6.51
plotGenome       5.92   0.02    5.95
readMeths        5.44   0.37    5.81
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'segmentSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'segmentSeq'
    finding HTML links ... done
    SL                                      html  
    alignmentClass-class                    html  
    alignmentData-class                     html  
    alignmentMeth-class                     html  
    averageMethylationRegions               html  
    finding level-2 HTML links ... done

    classifySeg                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/classifySeg.Rd:45: missing file link 'getPriors.NB'
    findChunks                              html  
    getCounts                               html  
    getOverlaps                             html  
    givenExpression                         html  
    hSL                                     html  
    heuristicSeg                            html  
    lociData-class                          html  
    lociLikelihoods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/lociLikelihoods.Rd:27: missing file link 'getLikelihoods.NB'
    mergeMethSegs                           html  
    methData-class                          html  
    normaliseNC                             html  
    plotGenome                              html  
    plotMeth                                html  
    plotMethDistribution                    html  
    processAD                               html  
    readMethods                             html  
    readMeths                               html  
    segClass-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segClass-class.Rd:23: missing file link 'GRanges'
    segData-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segData-class.Rd:25: missing file link 'GRanges'
    segMeth-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAD7BeC/R.INSTALL39b48b65fb5/segmentSeq/man/segMeth-class.Rd:25: missing file link 'GRanges'
    segmentSeq-package                      html  
    selectLoci                              html  
    summariseLoci                           html  
    thresholdFinder                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.12.0.zip
* DONE (segmentSeq)
In R CMD INSTALL
In R CMD INSTALL