Package: MMDiff2

Version: 1.12.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MMDiff2_1.12.0.tar.gz

StartedAt: 2019-10-16 03:16:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:21:14 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 285.2 seconds

RetCode: 0

Status:  OK

CheckDir: MMDiff2.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MMDiff2_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MMDiff2.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MMDiff2’ 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DBAmmd: no visible global function definition for ‘new’
getReads: no visible global function definition for ‘IRangesList’
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
compDists        24.207  1.043  25.259
DBAmmd-Accessors  9.562  0.332   9.896
plotPeak          9.106  0.360  10.670
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MMDiff2.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MMDiff2
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MMDiff2’ ...
** using staged installation
** R
** data
** 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 (MMDiff2)

name	user	system	elapsed
Cfp1-Peaks	0.001	0.000	0.000
DBAmmd-Accessors	9.562	0.332	9.896
DBAmmd-class	0.032	0.000	0.055
MMD	0	0	0
compDists	24.207	1.043	25.259
compHists	3.237	0.096	3.334
compPvals	1.328	0.096	1.424
estimateFragmentCenters	1.708	0.072	1.779
getPeakReads	0.249	0.004	0.402
mm9-Genes	0	0	0
plotDISTS4Peak	1.68	0.16	1.84
plotDists	1.475	0.060	1.537
plotPeak	9.106	0.360	10.670
reportResults	1.832	0.072	1.905
runShinyMMDiff2	0	0	0
server.MMDiff2	0	0	0
ui.MMDiff2	0	0	0