BioC 3.4: CHECK report for S4Vectors on tokay1

Package: S4Vectors

Version: 0.12.2

Command: rm -rf S4Vectors.buildbin-libdir S4Vectors.Rcheck && mkdir S4Vectors.buildbin-libdir S4Vectors.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=S4Vectors.buildbin-libdir S4Vectors_0.12.2.tar.gz >S4Vectors.Rcheck\00install.out 2>&1 && cp S4Vectors.Rcheck\00install.out S4Vectors-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=S4Vectors.buildbin-libdir --install="check:S4Vectors-install.out" --force-multiarch --no-vignettes --timings S4Vectors_0.12.2.tar.gz

StartedAt: 2017-04-15 00:42:13 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:44:35 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 142.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: S4Vectors.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf S4Vectors.buildbin-libdir S4Vectors.Rcheck && mkdir S4Vectors.buildbin-libdir S4Vectors.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=S4Vectors.buildbin-libdir S4Vectors_0.12.2.tar.gz >S4Vectors.Rcheck\00install.out 2>&1 && cp S4Vectors.Rcheck\00install.out S4Vectors-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=S4Vectors.buildbin-libdir --install="check:S4Vectors-install.out" --force-multiarch --no-vignettes --timings S4Vectors_0.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/S4Vectors.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'S4Vectors/DESCRIPTION' ... OK
* this is package 'S4Vectors' version '0.12.2'
* 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 whether package 'S4Vectors' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.duplicated.List: no visible binding for global variable 'LogicalList'
aggregateWithDots: no visible global function definition for
  'PartitioningByEnd'
aggregateWithDots: no visible global function definition for
  'ManyToManyGrouping'
aggregateWithDots: no visible global function definition for
  'FactorList'
aggregateWithDots : <anonymous> : <anonymous>: no visible global
  function definition for 'extractList'
formulaAsListCall: no visible global function definition for 'terms'
hasS3Method: no visible global function definition for 'getS3method'
!,List: no visible binding for global variable 'RleList'
!,List: no visible binding for global variable 'LogicalList'
<=,List-List: no visible binding for global variable 'LogicalList'
<=,List-list: no visible binding for global variable 'LogicalList'
<=,list-List: no visible binding for global variable 'LogicalList'
==,List-List: no visible binding for global variable 'LogicalList'
==,List-list: no visible binding for global variable 'LogicalList'
==,list-List: no visible binding for global variable 'LogicalList'
duplicated,List: no visible binding for global variable 'LogicalList'
evalSeparately,FilterRules : <anonymous>: no visible global function
  definition for '.'
is.na,List: no visible binding for global variable 'RleList'
is.na,List: no visible binding for global variable 'LogicalList'
match,List-List: no visible binding for global variable 'RleList'
match,List-List: no visible binding for global variable 'IntegerList'
match,List-list: no visible binding for global variable 'RleList'
match,List-list: no visible binding for global variable 'IntegerList'
match,list-List: no visible binding for global variable 'RleList'
match,list-List: no visible binding for global variable 'IntegerList'
order,List: no visible binding for global variable 'IntegerList'
pcompare,List-List: no visible binding for global variable
  'IntegerList'
pcompare,List-list: no visible binding for global variable
  'IntegerList'
pcompare,list-List: no visible binding for global variable
  'IntegerList'
rank,List: no visible binding for global variable 'IntegerList'
Undefined global functions or variables:
  . FactorList IntegerList LogicalList ManyToManyGrouping
  PartitioningByEnd RleList extractList getS3method terms
Consider adding
  importFrom("stats", "terms")
  importFrom("utils", "getS3method")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'as.data.frame.DataTable' 'as.vector.Rle' 'colMeans' 'colSums'
  'droplevels.List' 'droplevels.Rle' 'duplicatedIntegerPairs'
  'duplicatedIntegerQuads' 'expand.grid' 'matchIntegerPairs'
  'matchIntegerQuads' 'orderIntegerPairs' 'orderIntegerQuads'
  'parallelSlotNames' 'pcompareRecursively' 'phead' 'ptail'
  'recycleArg' 'recycleCharacterArg' 'recycleLogicalArg' 'rowMeans'
  'rowSums' 'selectHits' 'selfmatchIntegerPairs'
  'selfmatchIntegerQuads'
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 'anyDuplicated' and siglist 'Rle'
  generic 'anyDuplicated' and siglist 'RleNSBS'
  generic 'anyNA' and siglist 'List'
  generic 'anyNA' and siglist 'Rle'
  generic 'anyNA' and siglist 'Vector'
  generic 'as.data.frame' and siglist 'DataTable'
  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,DataTableORNULL'
  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 'duplicated' and siglist 'List'
  generic 'eval' and siglist 'expression,Vector'
  generic 'eval' and siglist 'language,Vector'
  generic 'expand.grid' and siglist 'Vector'
  generic 'extractROWS' and siglist 'DataFrame,ANY'
  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 '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' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'setListElement' and siglist 'SimpleList'
  generic 'showAsCell' and siglist 'Date'
  generic 'showAsCell' and siglist 'POSIXt'
  generic 'sort' and siglist 'List'
  generic 'to' and siglist 'HitsList'
  generic 'transform' and siglist 'DataTable'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'with' and siglist 'Vector'
  generic 'xtabs' 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 '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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386/S4Vectors.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
shiftApply-methods 13.16   2.05    15.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
shiftApply-methods 14.27   2.89   17.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/S4Vectors.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1165:20: 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;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c List_class.c -o List_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'Rle_extract_range':
Rle_class.c:984:2: warning: 'Ltrim' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return extract_Rle_range(x_values, INTEGER(x_lengths),
  ^
Rle_class.c:984:2: warning: 'Rtrim' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c int_utils.c -o int_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c str_utils.c -o str_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def 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 vector_utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386
** 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 'rowSums' in package 'S4Vectors'
Creating a new generic function for 'colSums' in package 'S4Vectors'
Creating a new generic function for 'rowMeans' in package 'S4Vectors'
Creating a new generic function for 'colMeans' 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 '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 '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

install for x64

* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1165:20: 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;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c List_class.c -o List_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rle_class.c -o Rle_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c int_utils.c -o int_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c str_utils.c -o str_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def 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 vector_utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.12.2.zip
* DONE (S4Vectors)

name	user	system	elapsed
Annotated-class	0.61	0.00	0.61
DataFrame-class	0.2	0.0	0.2
DataTable-class	0.02	0.00	0.02
FilterRules-class	0.05	0.00	0.05
Hits-class	0.04	0.00	0.04
Hits-comparison	0.02	0.00	0.02
Hits-setops	0.06	0.00	0.06
List-class	0	0	0
List-utils	0.09	0.00	0.10
Pairs-class	0.04	0.00	0.03
Rle-class	0.03	0.00	0.03
Rle-runstat	0.07	0.00	0.08
Rle-utils	0.02	0.00	0.01
SimpleList-class	0.02	0.00	0.02
Vector-class	0	0	0
Vector-comparison	0.01	0.02	0.03
Vector-merge	1.10	0.01	1.11
Vector-setops	0	0	0
aggregate-methods	0.03	0.00	0.03
expand-methods	0.13	0.00	0.13
isSorted	0	0	0
shiftApply-methods	13.16	2.05	15.20
split-methods	0.05	0.00	0.05
str-utils	0	0	0
zip-methods	0.01	0.00	0.01

name	user	system	elapsed
Annotated-class	0.71	0.00	0.70
DataFrame-class	0.28	0.01	0.30
DataTable-class	0.04	0.00	0.03
FilterRules-class	0.06	0.02	0.08
Hits-class	0.08	0.00	0.07
Hits-comparison	0.03	0.00	0.04
Hits-setops	0.08	0.00	0.07
List-class	0	0	0
List-utils	0.12	0.00	0.13
Pairs-class	0.06	0.00	0.06
Rle-class	0.03	0.00	0.03
Rle-runstat	0.08	0.00	0.08
Rle-utils	0.02	0.02	0.03
SimpleList-class	0.01	0.00	0.02
Vector-class	0	0	0
Vector-comparison	0.05	0.00	0.04
Vector-merge	1.39	0.05	1.44
Vector-setops	0	0	0
aggregate-methods	0.06	0.00	0.06
expand-methods	0.19	0.00	0.19
isSorted	0	0	0
shiftApply-methods	14.27	2.89	17.16
split-methods	0.09	0.00	0.10
str-utils	0.02	0.00	0.01
zip-methods	0.03	0.00	0.03