BioC 3.2: CHECK report for GenomicTuples on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicTuples_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicTuples.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 ‘GenomicTuples/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicTuples’ version ‘1.4.0’
* 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 ‘GenomicTuples’ can be installed ... [24s/24s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::.strandAsSignedNumber’ ‘GenomicRanges:::clone’
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlots’
  ‘GenomicRanges:::extraColumnSlotsAsDF’ ‘GenomicRanges:::showList’
  ‘IRanges:::findOverlaps_NCList’ ‘IRanges:::min_overlap_score’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  ‘S4Vectors:::VH_recycle’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findEqual.GTuples: no visible global function definition for
  ‘splitRanges’
.findEqual.GTuples : <anonymous> : <anonymous>: no visible global
  function definition for ‘IRanges’
GTuples: no visible global function definition for ‘IRanges’
GTuplesList: no visible global function definition for
  ‘PartitioningByEnd’
tuples<-,GTuples : .local: no visible global function definition for
  ‘IRanges’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [55s/55s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  2. Failure (at test-GTuples-comparison.R#304): sort works ----------------------
  sort(q3) is not identical to q3[order(q3)]. Differences: 
  Attributes: < Component "internalPos": Mean relative difference: 0.5 >
  Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 0.25 > >
  
  testthat results ================================================================
  OK: 987 SKIPPED: 0 FAILED: 2
  1. Failure (at test-GTuples-comparison.R#294): rank works 
  2. Failure (at test-GTuples-comparison.R#304): sort works 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.


R version 3.2.2 Patched (2015-10-08 r69496) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("GenomicTuples")
Loading required package: GenomicTuples
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:testthat':

    compare

Loading required package: IRanges
Loading required package: GenomeInfoDb
1. Failure (at test-GTuples-comparison.R#294): rank works ----------------------
rank(sort(q3)) is not identical to seq_len(length(q3)). Differences: 
Mean relative difference: 0.1818182

2. Failure (at test-GTuples-comparison.R#304): sort works ----------------------
sort(q3) is not identical to q3[order(q3)]. Differences: 
Attributes: < Component "internalPos": Mean relative difference: 0.5 >
Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 0.25 > >

testthat results ================================================================
OK: 987 SKIPPED: 0 FAILED: 2
1. Failure (at test-GTuples-comparison.R#294): rank works 
2. Failure (at test-GTuples-comparison.R#304): sort works 

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘GenomicTuples’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GenomicTuples_init.c -o GenomicTuples_init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IPD.cpp -o IPD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c allTuplesSorted.cpp -o allTuplesSorted.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c compareGTuples.cpp -o compareGTuples.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o GenomicTuples.so GenomicTuples_init.o IPD.o RcppExports.o allTuplesSorted.o compareGTuples.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/GenomicTuples.Rcheck/GenomicTuples/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicTuples)

name	user	system	elapsed
GTuples-class	0.298	0.003	0.302
GTuples-comparison	1.253	0.004	1.257
GTuplesList-class	0.551	0.004	0.555
findOverlaps-methods	0.866	0.003	0.870
illdefined-methods	0.019	0.000	0.019
intra-tuple-methods	0.170	0.002	0.172
nearest-methods	0.778	0.003	0.781

BioC 3.2: CHECK report for GenomicTuples on perceval

Summary

Command output