BioC 3.0: CHECK report for MinimumDistance on oaxaca

Package: MinimumDistance

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.10.2.tar.gz

StartedAt: 2015-04-10 01:21:27 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:28:59 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 452.0 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MinimumDistance’ version ‘1.10.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .gigignore
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 ‘MinimumDistance’ can be installed ... [29s/30s] 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
FilterParamMD 24.054  1.760  25.903
pedigreeGrid   8.565  0.493   9.180
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [84s/85s]
 [84s/85s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘BSgenome.Hsapiens.UCSC.hg18’
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.

* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
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	0.025	0.001	0.026
FilterParamMD	24.054	1.760	25.903
MAP2	0.437	0.035	0.473
MDRanges-class	0.063	0.002	0.066
MinDistGRanges-class	0.114	0.002	0.116
MinDistGRanges	0.060	0.001	0.061
ParentOffspring-class	0.002	0.000	0.002
ParentOffspringList-class	0.003	0.000	0.003
Pedigree	0.011	0.000	0.010
TrioSet	1.721	0.044	1.789
acf2	0.004	0.000	0.004
md_exp	0.001	0.000	0.002
pedigreeGrid	8.565	0.493	9.180
pedigreeViewports	0.005	0.000	0.004