BioC 3.5: CHECK report for InteractionSet on veracruz2

Package: InteractionSet

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings InteractionSet_1.4.0.tar.gz

StartedAt: 2017-10-18 05:04:03 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:07:50 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 226.8 seconds

RetCode: 0

Status:  OK

CheckDir: InteractionSet.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 InteractionSet_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/InteractionSet.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InteractionSet/DESCRIPTION’ ... OK
* this is package ‘InteractionSet’ 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 ‘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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/InteractionSet.Rcheck/00check.log’
for details.

* installing *source* package ‘InteractionSet’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c box_bounds.cpp -o box_bounds.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c overlaps.cpp -o overlaps.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 InteractionSet.so box_bounds.o init.o overlaps.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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	1.510	0.060	1.616
ContactMatrix-class	0.102	0.000	0.106
ContactMatrix-distances	0.151	0.004	0.162
ContactMatrix-overlaps	0.597	0.009	0.628
ContactMatrix-sorting	0.376	0.004	0.390
ContactMatrix-subset	0.169	0.004	0.178
GInteractions-class	0.229	0.002	0.234
InteractionSet-class	0.303	0.003	0.315
boundingBox	0.331	0.003	0.349
conversion	0.794	0.009	0.822
distances	0.358	0.004	0.374
granges-methods	0.319	0.008	0.335
interaction-accessors	0.790	0.011	0.829
interaction-compare	0.839	0.008	0.874
interaction-subset	0.942	0.010	0.997
linearize	1.691	0.012	1.755
linkOverlaps	0.808	0.009	0.847
overlaps	1.375	0.016	1.437
pairs	0.610	0.007	0.647