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BioC 2.13: CHECK report for genomeIntervals on perceval

This page was generated on 2014-04-05 09:52:14 -0700 (Sat, 05 Apr 2014).

Package 297/750HostnameOS / ArchBUILDCHECKBUILD BIN
genomeIntervals 1.18.0
Julien Gagneur
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/genomeIntervals
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: genomeIntervals
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomeIntervals_1.18.0.tar.gz
StartedAt: 2014-04-05 01:33:51 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:35:11 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 80.7 seconds
RetCode: 0
Status:  OK 
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [5s/6s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’ [6s/6s]
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,36d12
< 
< 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':
< 
<     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
<     duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
<     lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
<     pmin, pmin.int, Position, rank, rbind, Reduce, 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’ [6s/6s]
  Running ‘fullShow.R’ [0s/0s]
 [12s/12s] 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.

genomeIntervals.Rcheck/00install.out:

* 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)

genomeIntervals.Rcheck/genomeIntervals-Ex.timings:

nameusersystemelapsed
GenomeIntervals-constructor0.1890.0020.194
Genome_intervals-class0.0920.0040.103
Genome_intervals-ordering0.1150.0030.119
Genome_intervals_stranded-class0.1160.0030.120
c.Genome_intervals0.1020.0040.108
core_annotated0.0560.0020.059
distance_to_nearest-methods0.3990.0090.411
getGffAttribute0.7140.0940.848
interval_overlap-methods0.1540.0050.163
interval_set_operations-methods1.1190.0071.148
parseGffAttributes0.0700.0020.076
readGFF30.0960.0040.105