BioC 3.1: CHECK report for genomeIntervals on petty

Package: genomeIntervals

Version: 1.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomeIntervals_1.24.1.tar.gz

StartedAt: 2015-10-08 23:15:21 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:16:36 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 74.9 seconds

RetCode: 0

Status:  OK

CheckDir: genomeIntervals.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 genomeIntervals_1.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/genomeIntervals.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 ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.24.1’
* 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/5s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
interval_complement,Genome_intervals : .local: warning in
  factor(rep(as.character(fac.comb[, 2]), times = nrows), level =
  levels(seq_name(x))): partial argument match of 'level' to 'levels'
interval_complement,Genome_intervals_stranded : .local: warning in
  factor(rep(names(s), times = sapply(gi.list, nrow)), level =
  levels(strand(x))): partial argument match of 'level' to 'levels'
* 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 files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’ [5s/5s]
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,34d12
< 
< 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,
<     do.call, 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, unsplit
< 
  Running ‘consistency-tests.R’ [5s/5s]
  Running ‘fullShow.R’ [1s/1s]
 [11s/11s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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
** installing vignettes
** testing if installed package can be loaded
* DONE (genomeIntervals)

name	user	system	elapsed
GenomeIntervals-constructor	0.113	0.001	0.115
Genome_intervals-class	0.095	0.001	0.097
Genome_intervals-ordering	0.123	0.001	0.124
Genome_intervals_stranded-class	0.091	0.002	0.092
c.Genome_intervals	0.143	0.006	0.150
core_annotated	0.071	0.002	0.073
distance_to_nearest-methods	0.325	0.002	0.348
getGffAttribute	0.670	0.097	0.914
interval_overlap-methods	0.215	0.002	0.217
interval_set_operations-methods	1.409	0.012	1.422
parseGffAttributes	0.063	0.001	0.065
readGFF3	0.062	0.002	0.064