BioC 2.13: CHECK report for genomeIntervals on zin1

Package: genomeIntervals

Version: 1.18.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings genomeIntervals_1.18.0.tar.gz

StartedAt: 2014-04-05 01:25:05 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:25:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 49.5 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.18.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genomeIntervals’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘genomeIntervals.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’ [4s/4s]
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,37d12
< 
< Attaching package: 'BiocGenerics'
< 
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< The following object is masked from 'package:stats':
< 
<     xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
<     get, intersect, is.unsorted, lapply, mapply, match, mget, order,
<     paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
<     rownames, sapply, setdiff, sort, table, tapply, union, unique,
<     unlist
< 
< Warning messages:
< 1: replacing previous import by 'intervals::coerce' when loading 'genomeIntervals' 
< 2: replacing previous import by 'intervals::initialize' when loading 'genomeIntervals' 
  Running ‘consistency-tests.R’ [4s/4s]
  Running ‘fullShow.R’ [0s/0s]
 [8s/8s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.

* installing *source* package ‘genomeIntervals’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘intervals::coerce’ when loading ‘genomeIntervals’
Warning: replacing previous import by ‘intervals::initialize’ when loading ‘genomeIntervals’
* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.124	0.000	0.124
Genome_intervals-class	0.096	0.012	0.108
Genome_intervals-ordering	0.092	0.000	0.091
Genome_intervals_stranded-class	0.068	0.000	0.067
c.Genome_intervals	0.080	0.004	0.084
core_annotated	0.048	0.000	0.048
distance_to_nearest-methods	0.248	0.000	0.247
getGffAttribute	0.436	0.048	0.487
interval_overlap-methods	0.128	0.000	0.126
interval_set_operations-methods	0.896	0.004	0.904
parseGffAttributes	0.048	0.000	0.048
readGFF3	0.116	0.004	0.119