BioC 3.2: CHECK report for GenomicFiles on perceval

Package: GenomicFiles

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFiles_1.5.5.tar.gz

StartedAt: 2015-08-24 01:05:22 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:10:43 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 320.6 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_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.5.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘BiocParallel’
  ‘Rsamtools’ ‘rtracklayer’
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 ... [21s/21s] 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 ... [187s/102s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
reduceByFile-methods  49.899 19.935  26.367
reduceByRange-methods 23.807  9.823  15.786
reduceByYield         15.077  4.959  36.273
pack-methods           7.340  4.607   1.092
GenomicFiles-class     6.670  2.858   8.445
unpack-methods         3.290  2.057   2.961
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFiles_unit_tests.R’ [10s/10s]
 [10s/10s] 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-3.2-bioc/meat/GenomicFiles.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicFiles’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFiles)

name	user	system	elapsed
BamFileViews-class	0.001	0.000	0.001
BigWigFileViews-class	0.000	0.000	0.001
FaFileViews-class	0.000	0.000	0.001
GenomicFileViews-class	0.001	0.000	0.001
GenomicFiles-class	6.670	2.858	8.445
pack-methods	7.340	4.607	1.092
reduceByFile-methods	49.899	19.935	26.367
reduceByRange-methods	23.807	9.823	15.786
reduceByYield	15.077	4.959	36.273
registry-utils	0.002	0.000	0.003
unpack-methods	3.290	2.057	2.961