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BioC 3.5: CHECK report for genomeIntervals on malbec2

This page was generated on 2017-08-16 13:13:18 -0400 (Wed, 16 Aug 2017).

Package 535/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomeIntervals 1.32.0
Julien Gagneur
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/genomeIntervals
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomeIntervals
Version: 1.32.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings genomeIntervals_1.32.0.tar.gz
StartedAt: 2017-08-15 23:20:21 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:21:48 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:  OK 
CheckDir: genomeIntervals.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings genomeIntervals_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-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 ‘1.32.0’
* 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 ... 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 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’ ...13,35d12
< 
< 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, sd, var, xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
<     as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.


genomeIntervals.Rcheck/00install.out:

* 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)

genomeIntervals.Rcheck/genomeIntervals-Ex.timings:

nameusersystemelapsed
GenomeIntervals-constructor0.1760.0000.179
Genome_intervals-class0.0320.0000.034
Genome_intervals-coercion-methods000
Genome_intervals-ordering0.0600.0000.062
Genome_intervals_stranded-class0.0560.0000.059
c.Genome_intervals0.0800.0040.087
core_annotated0.0480.0040.054
distance_to_nearest-methods0.5240.0040.529
genomeIntervals-readGff30.4000.0240.427
getGffAttribute0.0520.0040.055
interval_overlap-methods0.1080.0040.114
interval_set_operations-methods0.6600.0040.665
parseGffAttributes0.0240.0000.024