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BioC 3.2: CHECK report for S4Vectors on oaxaca

This page was generated on 2015-10-27 17:41:24 -0400 (Tue, 27 Oct 2015).

Package 935/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
S4Vectors 0.8.0
Bioconductor Package Maintainer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/S4Vectors
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: S4Vectors
Version: 0.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings S4Vectors_0.8.0.tar.gz
StartedAt: 2015-10-27 07:40:59 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:42:25 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 86.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: S4Vectors.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings S4Vectors_0.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/S4Vectors.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘0.8.0’
* 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 ... [8s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘anyMissing’ ‘makePrettyMatrixForCompactPrinting’
  ‘new_SimpleList_from_list’
* checking S3 generic/method consistency ... WARNING
droplevels:
  function(x, ...)
droplevels.List:
  function(x, except)

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

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’
aggregate.List: no visible global function definition for
  ‘SimpleAtomicList’
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’
aggregate,List : .local: no visible global function definition for
  ‘SimpleAtomicList’
coerce,ANY-List: no visible global function definition for
  ‘PartitioningByEnd’
coerce,integer-List: no visible global function definition for
  ‘PartitioningByEnd’
evalSeparately,FilterRules : .local : <anonymous>: no visible global
  function definition for ‘.’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘anyDuplicated.WindowNSBS’ ‘as.vector.Rle’ ‘droplevels.List’
  ‘droplevels.Rle’ ‘filterRules’ ‘head.Vector’ ‘parallelSlotNames’ ‘pc’
  ‘phead’ ‘ptail’ ‘recycleArg’ ‘recycleCharacterArg’
  ‘recycleLogicalArg’ ‘selectHits’ ‘shiftApply’ ‘tail.Vector’
  ‘window.Vector’
Undocumented S4 methods:
  generic 'Rle' and siglist 'Rle,missing'
  generic 'anyDuplicated' and siglist 'Rle'
  generic 'anyDuplicated' and siglist 'WindowNSBS'
  generic 'anyNA' and siglist 'Rle'
  generic 'anyNA' and siglist 'Vector'
  generic 'as.integer' and siglist 'WindowNSBS'
  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 'eval' and siglist 'expression,Vector'
  generic 'eval' and siglist 'language,Vector'
  generic 'extractROWS' and siglist 'ANY,ANY'
  generic 'extractROWS' and siglist 'DataFrame,ANY'
  generic 'extractROWS' and siglist 'Hits,ANY'
  generic 'extractROWS' and siglist 'NULL,ANY'
  generic 'extractROWS' and siglist 'Rle,ANY'
  generic 'extractROWS' and siglist 'SimpleList,ANY'
  generic 'extractROWS' and siglist 'Vector,ANY'
  generic 'extractROWS' and siglist 'vectorORfactor,WindowNSBS'
  generic 'findMatches' and siglist 'ANY'
  generic 'getListElement' and siglist 'SimpleList'
  generic 'getListElement' and siglist 'list'
  generic 'grep' and siglist 'ANY,Rle'
  generic 'grepl' and siglist 'ANY,Rle'
  generic 'head' and siglist 'Vector'
  generic 'isStrictlySorted' and siglist 'Rle'
  generic 'isStrictlySorted' and siglist 'WindowNSBS'
  generic 'length' and siglist 'WindowNSBS'
  generic 'match' and siglist 'ANY,Rle'
  generic 'match' and siglist 'Rle,Rle'
  generic 'parallelSlotNames' and siglist 'Hits'
  generic 'parallelSlotNames' and siglist 'Vector'
  generic 'rank' and siglist 'Rle'
  generic 'rep' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'replaceROWS' and siglist 'SimpleList'
  generic 'setListElement' and siglist 'SimpleList'
  generic 'showAsCell' and siglist 'Date'
  generic 'showAsCell' and siglist 'POSIXt'
  generic 'tail' and siglist 'Vector'
  generic 'transform' and siglist 'DataTable'
  generic 'window' and siglist 'Vector'
  generic 'with' and siglist 'Vector'
  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 ... NOTE
File ‘S4Vectors/libs/S4Vectors.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘AEbufs.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘AEbufs.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘S4Vectors_unit_tests.R’ [9s/9s]
 [9s/9s] 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.


S4Vectors.Rcheck/00install.out:

* 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 DataFrame_class.c -o DataFrame_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 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 subsetting_internals.c -o subsetting_internals.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 DataFrame_class.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 subsetting_internals.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/S4Vectors.Rcheck/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
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 ‘window’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘with’ 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 ‘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 ‘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’
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘split’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (S4Vectors)

S4Vectors.Rcheck/S4Vectors-Ex.timings:

nameusersystemelapsed
Annotated-class0.9350.0180.954
DataFrame-class0.1370.0040.141
DataTable-class0.0240.0010.025
FilterRules-class0.0760.0010.077
Hits-class0.0150.0010.016
Hits-comparison0.0530.0010.053
Hits-setops0.1360.0020.138
List-class0.0020.0000.002
List-utils0.1010.0070.108
Rle-class0.0640.0040.068
Rle-runstat0.1100.0020.112
Rle-utils0.0140.0000.015
SimpleList-class0.0410.0020.042
Vector-class0.0020.0000.003
Vector-comparison0.0430.0010.045
aggregate-methods0.0560.0010.057
isSorted0.0060.0000.006
split-methods0.0930.0020.094
str-utils0.0060.0010.007