BioC 3.3: CHECK report for GenomicTuples on morelia

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicTuples.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.0’
* 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 ... [15s/15s] 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:::VH_recycle’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  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: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
  IRanges PartitioningByEnd splitRanges
* 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [33s/33s]
 [34s/34s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicTuples’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GenomicTuples_init.c -o GenomicTuples_init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IPD.cpp -o IPD.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c allTuplesSorted.cpp -o allTuplesSorted.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c compareGTuples.cpp -o compareGTuples.o
clang++ -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 -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-3.3-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	0.209	0.005	0.214
GTuples-comparison	0.709	0.002	0.711
GTuplesList-class	0.288	0.002	0.290
findOverlaps-methods	0.486	0.002	0.487
illdefined-methods	0.010	0.000	0.011
intra-tuple-methods	0.089	0.001	0.090
nearest-methods	0.428	0.002	0.429

BioC 3.3: CHECK report for GenomicTuples on morelia

Summary

Command output