BioC 3.4: CHECK report for genomeIntervals on morelia

Package: genomeIntervals

Version: 1.30.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomeIntervals_1.30.1.tar.gz

StartedAt: 2017-04-15 02:41:44 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:43:41 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 117.7 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_1.30.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.30.1’
* 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 ... 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: 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: warning in
  factor(rep(names(s), times = sapply(gi.list, nrow)), level =
  levels(strand(x))): partial argument match of 'level' to 'levels'
coerce,Genome_intervals-RangedData: no visible global function
  definition for ‘na.omit’
writeGff3,data.frame: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’
  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':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
<     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
<     unique, unsplit, which, which.max, which.min
< 
  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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	0.104	0.001	0.105
Genome_intervals-class	0.068	0.001	0.069
Genome_intervals-coercion-methods	0.001	0.000	0.001
Genome_intervals-ordering	0.120	0.002	0.121
Genome_intervals_stranded-class	0.076	0.001	0.078
c.Genome_intervals	0.100	0.004	0.104
core_annotated	0.054	0.002	0.056
distance_to_nearest-methods	0.296	0.003	0.322
genomeIntervals-readGff3	0.681	0.086	0.772
getGffAttribute	0.056	0.001	0.058
interval_overlap-methods	0.150	0.002	0.152
interval_set_operations-methods	0.952	0.004	0.959
parseGffAttributes	0.044	0.001	0.046