Package: segmentSeq

Version: 2.14.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings segmentSeq_2.14.0.tar.gz

StartedAt: 2018-10-16 03:38:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:42:15 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 249.3 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings segmentSeq_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/segmentSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.14.0’
* 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 ... NOTE
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'segmentSeq'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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     27.648  0.068  27.739
lociLikelihoods 12.348  0.000  12.355
heuristicSeg    11.888  0.000  11.895
plotGenome       5.728  0.008   5.740
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL segmentSeq
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* installing to library ‘/home/biocbuild/bbs-3.7-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	3.092	0.000	3.140
classifySeg	27.648	0.068	27.739
findChunks	2.868	0.000	2.868
getCounts	4.632	0.008	4.644
getOverlaps	3.028	0.000	3.031
heuristicSeg	11.888	0.000	11.895
lociLikelihoods	12.348	0.000	12.355
normaliseNC	4.132	0.044	4.213
plotGenome	5.728	0.008	5.740
processAD	3.568	0.000	3.573
readMethods	2.808	0.000	2.809
readMeths	2.480	0.020	2.502
segData-class	3.480	0.004	3.486
segmentSeq-package	3.448	0.000	3.451
thresholdFinder	2.484	0.024	2.512