BioC 3.1: CHECK report for GenomicFiles on petty

Package: GenomicFiles

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFiles_1.4.0.tar.gz

StartedAt: 2015-10-08 23:15:32 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:20:58 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 326.0 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFiles.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 GenomicFiles_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicFiles.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘Rsamtools’ ‘GenomicRanges’
  ‘rtracklayer’ ‘BiocParallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFiles’ can be installed ... [22s/24s] 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
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [91s/106s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
reduceByFile-methods  29.921  1.207  31.571
reduceByRange-methods 18.070  0.333  18.414
reduceByYield          5.739  1.819  28.166
BigWigFileViews-class  6.084  0.013   6.130
GenomicFiles-class     5.604  0.146   6.329
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFiles_unit_tests.R’ [10s/10s]
 [11s/11s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicFiles.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicFiles’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GenomicFiles)

name	user	system	elapsed
BamFileViews-class	0.289	0.008	0.333
BigWigFileViews-class	6.084	0.013	6.130
FaFileViews-class	0.043	0.002	0.048
GenomicFileViews-class	0.136	0.001	0.138
GenomicFiles-class	5.604	0.146	6.329
pack-methods	1.251	0.023	1.276
reduceByFile-methods	29.921	1.207	31.571
reduceByRange-methods	18.070	0.333	18.414
reduceByYield	5.739	1.819	28.166
registry-utils	0.003	0.000	0.003
unpack-methods	2.993	1.995	2.892