BioC 3.6: CHECK report for MinimumDistance on veracruz1

Package: MinimumDistance

Version: 1.21.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MinimumDistance_1.21.2.tar.gz

StartedAt: 2017-08-16 05:39:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:44:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 292.7 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MinimumDistance_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* this is package ‘MinimumDistance’ version ‘1.21.2’
* 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 ‘MinimumDistance’ 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 loading without being on the library search path ... 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
callDenovoSegments: no visible global function definition for
  ‘read.bsfiles’
pruneTrioSet: no visible global function definition for
  ‘RangedDataList’
read.bsfiles2: no visible binding for global variable ‘read.bsfiles’
GenomeAnnotatedDataFrameFrom,character: no visible global function
  definition for ‘read.bsfiles’
calculateMindist,list: no visible binding for global variable ‘elt’
Undefined global functions or variables:
  RangedDataList elt read.bsfiles
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
FilterParamMD 3.855  0.127    7.03
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* 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-3.6-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.

* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘allNames’ in package ‘MinimumDistance’
Creating a generic function for ‘colMads’ from package ‘matrixStats’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)

name	user	system	elapsed
DNAcopyParam	0.016	0.000	0.018
FilterParamMD	3.855	0.127	7.030
MAP2	0.052	0.006	0.067
MDRanges-class	0.046	0.001	0.049
MinDistGRanges-class	0.100	0.002	0.108
MinDistGRanges	0.141	0.000	0.149
ParentOffspring-class	0.002	0.001	0.002
ParentOffspringList-class	0.002	0.000	0.002
Pedigree	0.007	0.000	0.009
TrioSet	2.556	0.050	3.350
acf2	0.004	0.000	0.022
md_exp	0.002	0.001	0.002
pedigreeGrid	3.759	0.153	4.730
pedigreeViewports	0.017	0.000	0.018