Package: dmrseq

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings dmrseq_1.6.0.tar.gz

StartedAt: 2020-04-15 05:30:23 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:36:37 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 374.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dmrseq.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings dmrseq_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/dmrseq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dmrseq’ version ‘1.6.0’
* 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 ‘dmrseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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
plotDMRs: warning in rank(as.numeric(rowSums(cov.unique)), ties =
  "first"): partial argument match of 'ties' to 'ties.method'
plotEmpiricalDistribution: no visible binding for global variable ‘wt’
Undefined global functions or variables:
  wt
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                            user system elapsed
dmrseq                    37.560  6.324  21.057
getAnnot                  16.992  0.584  19.244
plotEmpiricalDistribution  7.300  0.144   7.449
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/dmrseq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL dmrseq
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘dmrseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (dmrseq)

name	user	system	elapsed
BS.chr21	1.368	0.076	1.444
annot.chr21	0.000	0.000	0.001
dmrs.ex	0.004	0.000	0.002
dmrseq	37.560	6.324	21.057
getAnnot	16.992	0.584	19.244
meanDiff	0.576	0.020	0.595
plotDMRs	0.864	0.040	0.905
plotEmpiricalDistribution	7.300	0.144	7.449
simDMRs	3.652	0.036	3.691