S4Vectors 0.14.3
Bioconductor Package Maintainer
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/S4Vectors | | Last Changed Rev: 131934 / Revision: 131943 | | Last Changed Date: 2017-08-15 12:07:20 -0400 (Tue, 15 Aug 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings S4Vectors_0.14.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/S4Vectors.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.14.3’
* package encoding: UTF-8
* 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 ... 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:
‘data.table:::as.data.frame.data.table’
‘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
median:
function(x, na.rm, ...)
median.Rle:
function(x, na.rm)
median:
function(x, na.rm, ...)
median.Rle:
function(x, na.rm)
median:
function(x, na.rm, ...)
median.Rle:
function(x, na.rm)
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
aggregateWithDots: no visible global function definition for
‘PartitioningByEnd’
evalSeparately,FilterRules : <anonymous>: no visible global function
definition for ‘.’
Undefined global functions or variables:
. PartitioningByEnd
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘as.matrix.Vector’ ‘head.Linteger’ ‘parallelSlotNames’
‘pcompareRecursively’ ‘phead’ ‘ptail’ ‘selectHits’ ‘tail.Linteger’
‘window.Linteger’
Undocumented S4 classes:
‘integer_OR_Linteger’
Undocumented S4 methods:
generic '!' and siglist 'List'
generic '<=' and siglist 'List,List'
generic '<=' and siglist 'List,list'
generic '<=' and siglist 'list,List'
generic '==' and siglist 'List,List'
generic '==' and siglist 'List,list'
generic '==' and siglist 'list,List'
generic 'NSBS' and siglist 'Rle'
generic '[' and siglist 'Linteger'
generic 'anyDuplicated' and siglist 'Rle'
generic 'anyDuplicated' and siglist 'RleNSBS'
generic 'anyNA' and siglist 'List'
generic 'anyNA' and siglist 'Rle'
generic 'as.integer' and siglist 'NSBS'
generic 'as.integer' and siglist 'RleNSBS'
generic 'as.matrix' and siglist 'Vector'
generic 'by' and siglist 'Vector'
generic 'coerce' and siglist 'ANY,DataTable_OR_NULL'
generic 'countMatches' and siglist 'ANY'
generic 'do.call' and siglist 'ANY,List'
generic 'droplevels' and siglist 'DataFrame'
generic 'duplicated' and siglist 'List'
generic 'eval' and siglist 'expression,Vector'
generic 'eval' and siglist 'language,Vector'
generic 'extractROWS' and siglist 'DataFrame,ANY'
generic 'extractROWS' and siglist 'Linteger,ANY'
generic 'extractROWS' and siglist 'Linteger,NSBS'
generic 'extractROWS' and siglist 'Linteger,RangeNSBS'
generic 'extractROWS' and siglist 'Rle,NSBS'
generic 'extractROWS' and siglist 'Rle,RleNSBS'
generic 'extractROWS' and siglist 'SortedByQueryHits,ANY'
generic 'extractROWS' and siglist 'Vector,ANY'
generic 'from' and siglist 'HitsList'
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 'Linteger'
generic 'is.na' and siglist 'List'
generic 'is.unsorted' and siglist 'List'
generic 'isStrictlySorted' and siglist 'Rle'
generic 'isStrictlySorted' and siglist 'RleNSBS'
generic 'length' and siglist 'RleNSBS'
generic 'match' and siglist 'ANY,Rle'
generic 'match' and siglist 'List,List'
generic 'match' and siglist 'List,Vector'
generic 'match' and siglist 'List,list'
generic 'match' and siglist 'List,vector'
generic 'match' and siglist 'Rle,Rle'
generic 'match' and siglist 'list,List'
generic 'order' and siglist 'List'
generic 'parallelSlotNames' and siglist 'FilterRules'
generic 'parallelSlotNames' and siglist 'SimpleList'
generic 'parallelSlotNames' and siglist 'Vector'
generic 'pcompare' and siglist 'List,List'
generic 'pcompare' and siglist 'List,list'
generic 'pcompare' and siglist 'list,List'
generic 'pcompareRecursively' and siglist 'List'
generic 'pcompareRecursively' and siglist 'list'
generic 'rank' and siglist 'List'
generic 'rank' and siglist 'Rle'
generic 'rep.int' and siglist 'Linteger'
generic 'rep.int' and siglist 'Vector'
generic 'rep' and siglist 'DataFrame'
generic 'replaceROWS' and siglist 'DataFrame'
generic 'replaceROWS' and siglist 'Rle'
generic 'setListElement' and siglist 'SimpleList'
generic 'sort' and siglist 'DataTable'
generic 'sort' and siglist 'List'
generic 'tail' and siglist 'Linteger'
generic 'to' and siglist 'HitsList'
generic 'transform' and siglist 'Vector'
generic 'unique' and siglist 'List'
generic 'unique' and siglist 'SimpleList'
generic 'window' and siglist 'Linteger'
generic 'with' and siglist 'Vector'
generic 'xtabs' and siglist 'Vector'
generic 'xtfrm' and siglist 'Rle'
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 'List-utils'
‘deparse.level’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
shiftApply-methods 11.304 0.188 11.497
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.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: 3 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
from ../inst/include/S4Vectors_defines.h:18,
from S4Vectors.h:1,
from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1214:20: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^
Hits_class.c:218:12: note: ‘revmap’ was declared here
SEXP ans, revmap, symbol;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Linteger_class.c -o Linteger_class.o
Linteger_class.c: In function ‘llints_summary’:
Linteger_class.c:738:38: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (res == NA_LINTEGER || in_elt < res)
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c List_class.c -o List_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_class.c -o Rle_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c eval_utils.c -o eval_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_utils.c -o hash_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c int_utils.c -o int_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c logical_utils.c -o logical_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function]
static void sort_uchar_array(unsigned char *x, int nelt, int desc)
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c str_utils.c -o str_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o Linteger_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 map_ranges_to_runs.o safe_arithm.o sort_utils.o str_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/S4Vectors.Rcheck/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ 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 ‘setequal’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ 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 ‘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’
in method for ‘coerce’ with signature ‘"data.table","DataFrame"’: no definition for class “data.table”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (S4Vectors)