Multiple platform build/check report for BioC 3.9 - INSTALL report for S4Vectors on tokay2

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/S4Vectors_0.22.1.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.22.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.22.1.zip && rm S4Vectors_0.22.1.tar.gz S4Vectors_0.22.1.zip
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install for i386

* installing *source* package 'S4Vectors' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_increase_buflength':
AEbufs.c:31:2: warning: large integer implicitly truncated to unsigned type [-Woverflow]
  return MAX_BUFLENGTH;
  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include/Rinternals.h:1402:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define defineVar  Rf_defineVar
                    ^
Hits_class.c:216:12: note: 'revmap' was declared here
  SEXP ans, revmap, symbol;
            ^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (nodup0 && is_used->elts[ans_elt - 1])
                        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   if (sprintf(val_buf, "%lld", from_elt) < 0)
   ^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'check_integer_runs':
Rle_class.c:218:20: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *max_len_out_p = len_out;
                    ^
Rle_class.c: In function '_construct_character_Rle':
Rle_class.c:509:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     len_out += len_in;
             ^
Rle_class.c:489:30: note: 'len_out' was declared here
  unsigned long long int sum, len_out;
                              ^
Rle_class.c: In function '_construct_raw_Rle':
Rle_class.c:606:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     len_out += len_in;
             ^
Rle_class.c:587:30: note: 'len_out' was declared here
  unsigned long long int sum, len_out;
                              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c raw_utils.c -o raw_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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 LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/S4Vectors.buildbin-libdir/00LOCK-S4Vectors/00new/S4Vectors/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'normalizeSingleBracketReplacementValue' with signature '"List"': no definition for class "List"
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
  converting help for package 'S4Vectors'
    finding HTML links ... done
    Annotated-class                         html  
    DataFrame-class                         html  
    DataTable-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/DataTable-class.Rd:56: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    FilterMatrix-class                      html  
    FilterRules-class                       html  
    Hits-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-class.Rd:80: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-class.Rd:176: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-class.Rd:187: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-class.Rd:282: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-class.Rd:285: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
    Hits-comparison                         html  
    Hits-setops                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
    HitsList-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:101: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/HitsList-class.Rd:103: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    LLint-class                             html  
    List-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:59: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:73: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:74: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:75: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:83: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:84: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:85: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:95: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:144: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:152: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:205: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:206: file link 'LogicalList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:206: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:207: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:208: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:208: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:258: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:261: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:261: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-class.Rd:262: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    List-utils                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:94: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:105: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:115: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:127: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:156: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:189: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:192: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:207: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:210: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/List-utils.Rd:214: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
    Pairs-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Pairs-class.Rd:47: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Pairs-class.Rd:48: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Pairs-class.Rd:106: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
    Rle-class                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Rle-class.Rd:202: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Rle-class.Rd:221: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Rle-class.Rd:363: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
    Rle-runstat                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Rle-runstat.Rd:95: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
    Rle-utils                               html  
    S4Vectors-internals                     html  
    SimpleList-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/SimpleList-class.Rd:85: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/SimpleList-class.Rd:89: file link 'SimpleIntegerList' in package 'IRanges' does not exist and so has been treated as a topic
    Vector-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-class.Rd:213: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-class.Rd:221: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-class.Rd:356: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-class.Rd:371: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-class.Rd:372: file link 'XRaw' in package 'XVector' does not exist and so has been treated as a topic
    Vector-comparison                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-comparison.Rd:292: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-comparison.Rd:325: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-comparison.Rd:341: missing file link 'IntegerRanges-comparison'
    Vector-merge                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-merge.Rd:22: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-merge.Rd:22: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    Vector-setops                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-setops.Rd:90: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-setops.Rd:91: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/Vector-setops.Rd:92: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
    aggregate-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:38: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:38: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:42: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:44: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:45: file link 'SimpleAtomicList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:96: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/aggregate-methods.Rd:97: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
    character-utils                         html  
    expand-methods                          html  
    integer-utils                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/integer-utils.Rd:70: file link 'seq_len' in package 'base' does not exist and so has been treated as a topic
    isSorted                                html  
    shiftApply-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/shiftApply-methods.Rd:44: file link 'window' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/shiftApply-methods.Rd:45: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
    show-utils                              html  
    split-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/split-methods.Rd:47: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpm2Mgn2/R.INSTALL61833afd7c/S4Vectors/man/split-methods.Rd:64: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
    subsetting-utils                        html  
    zip-methods                             html  
** building package indices
** installing vignettes
   'RleTricks.Rnw' using 'UTF-8' 
   'S4QuickOverview.Rnw' using 'UTF-8' 
   'S4VectorsOverview.Rnw' using 'UTF-8' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include/Rinternals.h:1402:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define defineVar  Rf_defineVar
                    ^
Hits_class.c:216:12: note: 'revmap' was declared here
  SEXP ans, revmap, symbol;
            ^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (nodup0 && is_used->elts[ans_elt - 1])
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   if (sprintf(val_buf, "%lld", from_elt) < 0)
   ^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
LLint_class.c: In function 'llints_summary':
LLint_class.c:791:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res = _safe_llint_mult(res, in_elt);
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c raw_utils.c -o raw_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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 LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.22.1.zip
* DONE (S4Vectors)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
INSTALL report for S4Vectors on tokay2

Summary

Command output
