BioC 3.0: CHECK report for S4Vectors on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch S4Vectors_0.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/S4Vectors.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.4.0’
* 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 ‘S4Vectors’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘stats’ ‘stats4’ ‘BiocGenerics’
A package should be listed in only one of these fields.
* 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:
  ‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
droplevels:
  function(x, ...)
droplevels.Rle:
  function(x)

droplevels:
  function(x, ...)
droplevels.List:
  function(x, except)

droplevels:
  function(x, ...)
droplevels.Rle:
  function(x)

droplevels:
  function(x, ...)
droplevels.List:
  function(x, except)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fast_subset_List_by_LL: no visible global function definition for
  ‘PartitioningByEnd’
.fast_subset_List_by_NL: no visible global function definition for
  ‘PartitioningByEnd’
.fast_subset_List_by_RL: no visible global function definition for
  ‘PartitioningByEnd’
.unlist_NL_subscript: no visible global function definition for
  ‘PartitioningByEnd’
.unlist_RL_subscript: no visible global function definition for
  ‘PartitioningByEnd’
.unlist_RL_subscript: no visible global function definition for ‘shift’
pc: no visible binding for global variable ‘togroup’
pc: no visible global function definition for ‘splitAsList’
phead: no visible global function definition for ‘IRanges’
phead: no visible global function definition for ‘PartitioningByEnd’
ptail: no visible global function definition for ‘IRanges’
ptail: no visible global function definition for ‘PartitioningByEnd’
coerce,ANY-List: no visible global function definition for
  ‘PartitioningByEnd’
coerce,integer-List: no visible global function definition for
  ‘PartitioningByEnd’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘parallelSlotnames’ ‘pc’ ‘phead’ ‘ptail’ ‘shiftApply’
Undocumented S4 methods:
  generic 'Rle' and siglist 'Rle,missing'
  generic 'anyDuplicated' and siglist 'Rle'
  generic 'anyNA' and siglist 'Rle'
  generic 'anyNA' and siglist 'Vector'
  generic 'countMatches' and siglist 'ANY'
  generic 'do.call' and siglist 'ANY,List'
  generic 'droplevels' and siglist 'DataFrame'
  generic 'droplevels' and siglist 'List'
  generic 'droplevels' and siglist 'Rle'
  generic 'extractROWS' and siglist 'DataFrame'
  generic 'extractROWS' and siglist 'Rle'
  generic 'extractROWS' and siglist 'SimpleList'
  generic 'extractROWS' and siglist 'Vector'
  generic 'findMatches' and siglist 'ANY'
  generic 'getListElement' and siglist 'SimpleList'
  generic 'isStrictlySorted' and siglist 'Rle'
  generic 'parallelSlotnames' and siglist 'Hits'
  generic 'parallelSlotnames' and siglist 'Vector'
  generic 'rank' and siglist 'Rle'
  generic 'rank' and siglist 'Vector'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'NULL'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'replaceROWS' and siglist 'SimpleList'
  generic 'replaceROWS' and siglist 'matrix'
  generic 'setListElement' and siglist 'SimpleList'
  generic 'showAsCell' and siglist 'Date'
  generic 'showAsCell' and siglist 'POSIXt'
  generic 'transform' and siglist 'DataTable'
  generic 'xtfrm' and siglist 'Rle'
  generic 'xtfrm' and siglist 'Vector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'Rle-runstat'
  ‘y’ ‘algorithm’ ‘print.level’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘S4Vectors_unit_tests.R’ [7s/7s]
 [7s/7s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.

* installing *source* package ‘S4Vectors’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c AEbufs.c -o AEbufs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Hits_class.c -o Hits_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c List_class.c -o List_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rle_class.c -o Rle_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rle_utils.c -o Rle_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c SEXP_utils.c -o SEXP_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c SimpleList_class.c -o SimpleList_class.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c eval_utils.c -o eval_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hash_utils.c -o hash_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c int_utils.c -o int_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c logical_utils.c -o logical_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c safe_arithm.c -o safe_arithm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sort_utils.c -o sort_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c str_utils.c -o str_utils.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c vector_utils.c -o vector_utils.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 S4Vectors.so AEbufs.o Hits_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/S4Vectors.Rcheck/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘subset’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘transform’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘by’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.table’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘t’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘which’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘droplevels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘within’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (S4Vectors)

name	user	system	elapsed
Annotated-class	1.653	0.026	1.685
DataFrame-class	0.334	0.010	0.346
DataTable-class	0.047	0.003	0.049
Hits-class	0.001	0.001	0.001
List-class	0.002	0.000	0.002
List-utils	0.122	0.004	0.127
Rle-class	0.060	0.002	0.062
Rle-runstat	0.120	0.001	0.122
Rle-utils	0.021	0.001	0.022
SimpleList-class	0.052	0.003	0.054
Vector-class	0.002	0.000	0.002
Vector-comparison	0.074	0.002	0.076
isSorted	0.007	0.001	0.007
str-utils	0.007	0.001	0.007

BioC 3.0: CHECK report for S4Vectors on oaxaca

Summary

Command output