BioC 3.4: CHECK report for InteractionSet on malbec1

Package: InteractionSet

Version: 1.2.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings InteractionSet_1.2.1.tar.gz

StartedAt: 2017-04-14 23:20:14 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:23:11 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 176.9 seconds

RetCode: 0

Status:  OK

CheckDir: InteractionSet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings InteractionSet_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/InteractionSet.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InteractionSet/DESCRIPTION’ ... OK
* this is package ‘InteractionSet’ version ‘1.2.1’
* 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 ‘InteractionSet’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’ ‘S4Vectors:::disableValidity’
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  ‘S4Vectors:::selectSome’
  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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.4-bioc/meat/InteractionSet.Rcheck/00check.log’
for details.

* installing *source* package ‘InteractionSet’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c box_bounds.cpp -o box_bounds.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c overlaps.cpp -o overlaps.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o InteractionSet.so box_bounds.o init.o overlaps.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/InteractionSet.Rcheck/InteractionSet/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 (InteractionSet)

name	user	system	elapsed
ContactMatrix-accessors	0.712	0.012	0.727
ContactMatrix-class	0.064	0.004	0.065
ContactMatrix-distances	0.112	0.004	0.116
ContactMatrix-overlaps	0.292	0.004	0.298
ContactMatrix-sorting	0.248	0.000	0.250
ContactMatrix-subset	0.160	0.012	0.170
GInteractions-class	0.148	0.000	0.149
InteractionSet-class	0.192	0.000	0.196
boundingBox	0.288	0.004	0.294
conversion	0.960	0.008	0.969
distances	0.308	0.000	0.311
granges-methods	0.276	0.000	0.276
interaction-accessors	0.972	0.008	0.981
interaction-compare	0.736	0.000	0.737
interaction-subset	0.760	0.004	0.763
linearize	0.792	0.008	0.800
linkOverlaps	0.436	0.000	0.439
overlaps	1.144	0.008	1.151
pairs	0.512	0.004	0.517