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Package 245/609HostnameOS / ArchBUILDCHECKBUILD BIN
genomeIntervals 1.14.0
Julien Gagneur
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/genomeIntervals
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: genomeIntervals
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomeIntervals_1.14.0.tar.gz
StartedAt: 2013-03-24 23:41:54 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:43:04 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 70.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/genomeIntervals.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genomeIntervals/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomeIntervals' version '1.14.0'
* 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 whether package 'genomeIntervals' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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' ...13,29d12
< 
< Attaching package: 'BiocGenerics'
< 
< The following object(s) are masked from 'package:stats':
< 
<     xtabs
< 
< The following object(s) are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
<     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
<     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
<     rownames, sapply, setdiff, table, tapply, union, unique
< 
< Warning messages:
< 1: replacing previous import 'coerce' when loading 'intervals' 
< 2: replacing previous import 'initialize' when loading 'intervals' 
  Running 'consistency-tests.R'
  Running 'fullShow.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

genomeIntervals.Rcheck/00install.out:

* installing *source* package 'genomeIntervals' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'coerce' when loading 'intervals'
Warning: replacing previous import 'initialize' when loading 'intervals'
Creating a generic function for 'sort' from package 'base' in package 'genomeIntervals'
** help
*** installing help indices
** building package indices
** installing vignettes
   'genomeIntervals.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'coerce' when loading 'intervals'
Warning: replacing previous import 'initialize' when loading 'intervals'

* DONE (genomeIntervals)

genomeIntervals.Rcheck/genomeIntervals-Ex.timings:

nameusersystemelapsed
GenomeIntervals-constructor0.1000.0020.108
Genome_intervals-class0.0750.0010.077
Genome_intervals_stranded-class0.1140.0010.120
c.Genome_intervals0.1000.0080.126
core_annotated0.0500.0010.053
distance_to_nearest-methods0.2710.0030.278
getGffAttribute0.5260.1640.836
interval_overlap-methods0.1910.0030.199
interval_set_operations-methods1.3040.0081.322
parseGffAttributes0.0450.0020.047
readGFF30.0680.0020.071