BioC 3.2: CHECK report for genomeIntervals on perceval

Package: genomeIntervals

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomeIntervals_1.26.0.tar.gz

StartedAt: 2015-11-10 05:12:48 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:15:02 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 133.4 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.26.0’
* 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 ... [10s/11s] 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(seqnames(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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’ [7s/7s]
  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 objects are masked from 'package:stats':
< 
<     IQR, mad, 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, grep, grepl,
<     intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
<     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
<     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist, unsplit
< 
  Running ‘consistency-tests.R’ [7s/7s]
  Running ‘fullShow.R’ [0s/0s]
 [15s/15s] 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-3.2-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	0.077	0.002	0.079
Genome_intervals-class	0.058	0.002	0.060
Genome_intervals-coercion-methods	0.001	0.000	0.001
Genome_intervals-ordering	0.089	0.001	0.089
Genome_intervals_stranded-class	0.072	0.001	0.072
c.Genome_intervals	0.089	0.004	0.093
core_annotated	0.044	0.001	0.045
distance_to_nearest-methods	0.223	0.002	0.247
genomeIntervals-readGff3	0.523	0.075	0.598
getGffAttribute	0.041	0.001	0.043
interval_overlap-methods	0.117	0.001	0.118
interval_set_operations-methods	0.798	0.002	0.801
parseGffAttributes	0.038	0.000	0.038