Package: segmentSeq

Version: 2.16.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings segmentSeq_2.16.0.tar.gz

StartedAt: 2019-04-16 02:56:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:02:18 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 330.9 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings segmentSeq_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/segmentSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘segmentSeq’ 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
* 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 : <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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
classifySeg     32.332  0.076  32.465
lociLikelihoods 15.124  0.000  15.197
heuristicSeg    14.408  0.004  14.428
plotGenome       6.528  0.012   6.553
getCounts        5.404  0.000   5.412
normaliseNC      5.032  0.016   5.070
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL segmentSeq
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘segmentSeq’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	3.624	0.000	3.665
classifySeg	32.332	0.076	32.465
findChunks	3.328	0.004	3.337
getCounts	5.404	0.000	5.412
getOverlaps	3.616	0.000	3.634
heuristicSeg	14.408	0.004	14.428
lociLikelihoods	15.124	0.000	15.197
normaliseNC	5.032	0.016	5.070
plotGenome	6.528	0.012	6.553
processAD	4.248	0.000	4.253
readMethods	3.020	0.004	3.024
readMeths	3.108	0.032	3.144
segData-class	4.192	0.012	4.210
segmentSeq-package	4.364	0.000	4.395
thresholdFinder	3.668	0.064	3.742