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###
### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Biostrings_2.50.2.tar.gz && rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biostrings.buildbin-libdir Biostrings_2.50.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Biostrings_2.50.2.zip && rm Biostrings_2.50.2.tar.gz Biostrings_2.50.2.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 11.1M 100 11.1M 0 0 42.2M 0 --:--:-- --:--:-- --:--:-- 42.7M
install for i386
* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
IntAE *poffsets, *poffsets_order;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:124:3: warning: 'lkup_len' 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XString_class.c -o XString_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c inject_code.c -o inject_code.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_fasta_files.c -o read_fasta_files.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function 'parse_FASTQ_file':
read_fastq_files.c:310:8: warning: 'seq_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (data.length != seq_len) {
^
read_fastq_files.c:309:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (load_rec) {
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c strutils.c -o strutils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:136:29: 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:136:14: 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c xscat.c -o xscat.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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 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 read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'twoWayAlphabetFrequencyByQuality' with signature '"QualityScaledXStringSet"': no definition for class "QualityScaledXStringSet"
Creating a new generic function for 'strsplit' in package 'Biostrings'
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
converting help for package 'Biostrings'
finding HTML links ... done
AAString-class html
AMINO_ACID_CODE html
AlignedXStringSet-class html
Biostrings-internals html
DNAString-class html
GENETIC_CODE html
HNF4alpha html
IUPAC_CODE_MAP html
InDel-class html
MIndex-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/MIndex-class.Rd:94: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/MIndex-class.Rd:96: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/MIndex-class.Rd:98: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
MaskedXString-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/MaskedXString-class.Rd:182: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
MultipleAlignment-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/MultipleAlignment-class.Rd:122: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
PDict-class html
PairwiseAlignments-class html
PairwiseAlignments-io html
QualityScaledXStringSet-class html
RNAString-class html
XString-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XString-class.Rd:180: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XString-class.Rd:188: file link 'compact' in package 'XVector' does not exist and so has been treated as a topic
XStringPartialMatches-class html
XStringQuality-class html
XStringSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:92: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:179: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:199: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:201: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:207: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:213: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:218: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:219: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:220: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:331: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:331: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:334: file link 'compact' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-class.Rd:336: file link 'XVectorList' in package 'XVector' does not exist and so has been treated as a topic
XStringSet-comparison html
XStringSet-io html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSet-io.Rd:72: file link 'connection' in package 'base' does not exist and so has been treated as a topic
XStringSetList-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSetList-class.Rd:70: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSetList-class.Rd:77: file link 'elementNROWS' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringSetList-class.Rd:78: file link 'PartitioningByEnd' in package 'IRanges' does not exist and so has been treated as a topic
XStringViews-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/XStringViews-class.Rd:155: file link 'gaps' in package 'IRanges' does not exist and so has been treated as a topic
align-utils html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/align-utils.Rd:87: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
chartr html
detail html
dinucleotideFrequencyTest html
findPalindromes html
getSeq html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/getSeq.Rd:9: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/getSeq.Rd:19: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/getSeq.Rd:33: file link 'getSeq,BSgenome-method' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/getSeq.Rd:34: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/getSeq.Rd:39: file link 'getSeq,BSgenome-method' in package 'BSgenome' does not exist and so has been treated as a topic
gregexpr2 html
injectHardMask html
letter html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/letter.Rd:49: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
letterFrequency html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/letterFrequency.Rd:290: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
longestConsecutive html
lowlevel-matching html
maskMotif html
match-utils html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/match-utils.Rd:42: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/match-utils.Rd:48: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/match-utils.Rd:72: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/match-utils.Rd:74: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/match-utils.Rd:87: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
matchLRPatterns html
matchPDict-exact html
matchPDict-inexact html
matchPWM html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/matchPWM.Rd:84: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
matchPattern html
matchProbePair html
matchprobes html
misc html
needwunsQS html
nucleotideFrequency html
padAndClip html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/padAndClip.Rd:33: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/padAndClip.Rd:109: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
pairwiseAlignment html
phiX174Phage html
pid html
pmatchPattern html
replaceAt html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:36: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:37: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:43: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:52: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:53: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:72: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:98: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:103: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:110: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:110: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:115: file link 'unstrsplit' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:127: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:127: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:128: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceAt.Rd:128: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
replaceLetterAt html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceLetterAt.Rd:43: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/replaceLetterAt.Rd:130: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
reverseComplement html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/reverseComplement.Rd:48: file link 'reverse' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpu02bbk/R.INSTALL130c4df45934/Biostrings/man/reverseComplement.Rd:71: file link 'reverse' in package 'IRanges' does not exist and so has been treated as a topic
stringDist html
substitution_matrices html
toComplex html
translate html
trimLRPatterns html
xscat html
yeastSEQCHR1 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
IntAE *poffsets, *poffsets_order;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:124:3: warning: 'lkup_len' 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XString_class.c -o XString_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c inject_code.c -o inject_code.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_fasta_files.c -o read_fasta_files.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function 'parse_FASTQ_file':
read_fastq_files.c:310:8: warning: 'seq_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (data.length != seq_len) {
^
read_fastq_files.c:309:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (load_rec) {
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c strutils.c -o strutils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:110:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (if_ambig == TRANSLATE_ERROR) {
^
translate.c:136:29: note: 'if_ambig0' was declared here
int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
^
translate.c:106:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (if_non_ambig == TRANSLATE_TO_X)
^
translate.c:136:14: 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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c xscat.c -o xscat.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:98:21: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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 C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
from C:/Users/biocbuild/bbs-3.8-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':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:92:25: 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;
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:809:20: 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_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 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 read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biostrings' as Biostrings_2.50.2.zip
* DONE (Biostrings)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Biostrings' successfully unpacked and MD5 sums checked
In R CMD INSTALL
