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BioC 3.4: INSTALL report for Biostrings on moscato1

This page was generated on 2016-09-21 03:41:17 -0700 (Wed, 21 Sep 2016).

Package 125/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.41.4
H. Pagès
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 118619 / Revision: 121152
Last Changed Date: 2016-06-15 09:46:01 -0700 (Wed, 15 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.41.4
Command: rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/Biostrings_2.41.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=Biostrings.buildbin-libdir --merge-multiarch Biostrings_2.41.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL Biostrings_2.41.4.zip && rm Biostrings_2.41.4.tar.gz Biostrings_2.41.4.zip
StartedAt: 2016-09-19 20:39:02 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:41:06 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 123.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/Biostrings_2.41.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=Biostrings.buildbin-libdir --merge-multiarch Biostrings_2.41.4.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL Biostrings_2.41.4.zip  && rm Biostrings_2.41.4.tar.gz Biostrings_2.41.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 11.1M  100 11.1M    0     0  90.6M      0 --:--:-- --:--:-- --:--:-- 93.2M

install for i386

* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:179:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:109:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:799:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XString_class.c -o XString_class.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:243:30: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
       mappedStringPtr[index] = gapCodeValue;
                              ^
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:419:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:392:58: note: 'ans_col' was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:470:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:441:57: note: 'ans_elt' was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function 'build_Twobit':
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here
  SEXP ans, twobit_sign2pos;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:260:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:126:29: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:126:14: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
  ^
utils.c: In function '_get_twobit_signature_at':
utils.c:164:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XString_xscat':
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:18:13: note: 'ans_length' was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:20:14: note: 'ans_classname' was declared here
  const char *ans_classname;
              ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XStringSet_xscat':
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:66:32: note: 'ans_length' was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:68:14: note: 'ans_element_type' was declared here
  const char *ans_element_type;
              ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:179:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:109:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:799:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XString_class.c -o XString_class.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:225:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:419:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:392:58: note: 'ans_col' was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:470:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:441:57: note: 'ans_elt' was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function 'build_Twobit':
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here
  SEXP ans, twobit_sign2pos;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:260:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:101:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:126:29: note: 'if_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:97:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:126:14: note: 'if_non_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
  ^
utils.c: In function '_get_twobit_signature_at':
utils.c:164:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
In file included from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XString_xscat':
D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:94:21: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
                     ^
xscat.c:18:13: note: 'ans_length' was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:36:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
D:/biocbld/BBS-3˜1.4-B/R/include/Rinternals.h:661:20: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:20:14: note: 'ans_classname' was declared here
  const char *ans_classname;
              ^
In file included from D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XStringSet_xscat':
D:/biocbld/BBS-3˜1.4-B/R/include/Rdefines.h:88:25: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
                         ^
xscat.c:66:32: note: 'ans_length' was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
xscat.c:110:6: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (snprintf(ans_classname, sizeof(ans_classname),
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biostrings' as Biostrings_2.41.4.zip
* DONE (Biostrings)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'Biostrings' successfully unpacked and MD5 sums checked