Package: segmentSeq

Version: 2.18.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings segmentSeq_2.18.0.tar.gz

StartedAt: 2019-10-16 06:59:02 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:08:23 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 560.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: segmentSeq.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:segmentSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings segmentSeq_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/segmentSeq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.18.0'
* 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-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/classifySeg.Rd:45: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/lociLikelihoods.Rd:27: file link 'getLikelihoods.NB' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segClass-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segData-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segMeth-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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
* 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 ... NOTE
heuristicSeg : : 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
classifySeg     35.86   0.52   36.38
lociLikelihoods 17.09   0.00   17.13
heuristicSeg    16.00   0.00   16.00
plotGenome       6.27   0.03    6.37
getCounts        5.82   0.00    5.81
normaliseNC      5.16   0.54    5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifySeg        41.31   0.07   41.38
heuristicSeg       18.89   0.00   18.89
lociLikelihoods    18.53   0.00   18.54
getCounts           7.23   0.01    7.25
plotGenome          6.96   0.00    6.96
segmentSeq-package  5.48   0.00    5.48
segData-class       5.07   0.00    5.07
* 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-3.9-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/segmentSeq_2.18.0.tar.gz && rm -rf segmentSeq.buildbin-libdir && mkdir segmentSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=segmentSeq.buildbin-libdir segmentSeq_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL segmentSeq_2.18.0.zip && rm segmentSeq_2.18.0.tar.gz segmentSeq_2.18.0.zip
###
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install for i386

* installing *source* package 'segmentSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/classifySeg.Rd:45: file link 'getPriors.NB' in package 'baySeq' does not exist and so has been treated as a topic
    findChunks                              html  
    getCounts                               html  
    getOverlaps                             html  
    givenExpression                         html  
    hSL                                     html  
    heuristicSeg                            html  
    lociData-class                          html  
    lociLikelihoods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/lociLikelihoods.Rd:27: file link 'getLikelihoods.NB' in package 'baySeq' does not exist and so has been treated as a topic
    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-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segClass-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    segData-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segData-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    segMeth-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOT3zp/R.INSTALL12cc7f7c2e09/segmentSeq/man/segMeth-class.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    segmentSeq-package                      html  
    selectLoci                              html  
    summariseLoci                           html  
    thresholdFinder                         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 'segmentSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'segmentSeq' as segmentSeq_2.18.0.zip
* DONE (segmentSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'segmentSeq' successfully unpacked and MD5 sums checked