Package: segmentSeq

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings segmentSeq_2.21.0.tar.gz

StartedAt: 2020-01-16 08:43:54 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:52:32 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 518.2 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings segmentSeq_2.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.21.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
classifySeg        44.934  0.724  45.674
lociLikelihoods    19.552  0.108  19.887
heuristicSeg       18.706  0.063  18.770
plotGenome          8.889  0.075   8.965
getCounts           6.928  0.015   6.942
normaliseNC         5.551  1.094   6.648
readMeths           5.329  1.041   6.370
thresholdFinder     4.508  1.045   5.553
processAD           5.477  0.052   5.529
segData-class       5.395  0.031   5.426
segmentSeq-package  5.270  0.011   5.320
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL segmentSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘segmentSeq’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	4.349	0.034	4.387
classifySeg	44.934	0.724	45.674
findChunks	4.268	0.019	4.286
getCounts	6.928	0.015	6.942
getOverlaps	4.449	0.015	4.465
heuristicSeg	18.706	0.063	18.770
lociLikelihoods	19.552	0.108	19.887
normaliseNC	5.551	1.094	6.648
plotGenome	8.889	0.075	8.965
processAD	5.477	0.052	5.529
readMethods	4.337	0.014	4.350
readMeths	5.329	1.041	6.370
segData-class	5.395	0.031	5.426
segmentSeq-package	5.270	0.011	5.320
thresholdFinder	4.508	1.045	5.553