Package: genomeIntervals

Version: 1.8.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch genomeIntervals_1.8.0.tar.gz

StartedAt: 2011-10-20 14:34:16 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:35:40 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 83.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genomeIntervals.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/genomeIntervals.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'genomeIntervals' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'benchmarking-tests.R'
  Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ... OK
  Running 'consistency-tests.R'
  Running 'fullShow.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   genomeIntervals.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/genomeIntervals.Rcheck/00check.log'
for details

* installing *source* package 'genomeIntervals' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.1	0.0	0.1
Genome_intervals-class	0.11	0.00	0.11
Genome_intervals_stranded-class	0.09	0.00	0.09
c.Genome_intervals	0.09	0.00	0.09
core_annotated	0.07	0.00	0.07
distance_to_nearest-methods	0.28	0.00	0.28
getGffAttribute	0.42	0.14	12.92
interval_overlap-methods	0.17	0.00	0.17
interval_set_operations-methods	1.38	0.01	1.39
parseGffAttributes	0.04	0.00	0.05
readGFF3	0.07	0.00	0.06