############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Biostrings ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'Biostrings' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BAB_class.c -o BAB_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BitMatrix.c -o BitMatrix.o BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MIndex_class.c -o MIndex_class.o MIndex_class.c: In function 'SparseMIndex_endIndex': MIndex_class.c:184:27: warning: unused variable 'poffsets_order' [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SparseList_utils.c -o SparseList_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XStringSet_class.c -o XStringSet_class.o XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER': XStringSet_class.c:124:17: warning: 'lkup_len' may be used uninitialized [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ XStringSet_class.c:103:22: note: 'lkup_len' was declared here 103 | int ans_len, lkup_len, i; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XString_class.c -o XString_class.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_needwunsQS.c -o align_needwunsQS.o align_needwunsQS.c: In function 'align_needwunsQS': align_needwunsQS.c:155:29: warning: 'sc' may be used uninitialized [-Wmaybe-uninitialized] 155 | INTEGER(ans_elt)[0] = score; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~ align_needwunsQS.c:27:19: note: 'sc' was declared here 27 | int *sco, sc, n1, n2, i1, i2, j1, j2, al_buf_size; | ^~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_utils.c -o align_utils.o align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned': align_utils.c:250:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized] 250 | jPattern += indelWidthSubject; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:221:78: note: 'indelWidthSubject' was declared here 221 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:231:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized] 231 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { | ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:221:59: note: 'indelStartSubject' was declared here 221 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:239:72: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized] 239 | mappedStringPtr[index] = gapCodeValue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ align_utils.c:221:40: note: 'indelWidthPattern' was declared here 221 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:232:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized] 232 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:221:21: note: 'indelStartPattern' was declared here 221 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c find_palindromes.c -o find_palindromes.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtestsim.c -o gtestsim.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inject_code.c -o inject_code.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable] 956 | SEXP ans, ans_dimnames; | ^~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_PWM.c -o match_PWM.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern.c -o match_pattern.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pdict.c -o match_pdict.o In function 'vcount_PDict3Parts_XStringSet', inlined from 'vmatch_PDict3Parts_XStringSet' at match_pdict.c:508:10: match_pdict.c:419:33: warning: 'ans_col' may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet': match_pdict.c:392:65: note: 'ans_col' was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ In function 'vcount_XStringSet_XStringSet', inlined from 'vmatch_XStringSet_XStringSet' at match_pdict.c:542:10: match_pdict.c:470:41: warning: 'ans_elt' may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function 'vmatch_XStringSet_XStringSet': match_pdict.c:441:64: note: 'ans_elt' was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o match_pdict_ACtree2.c: In function 'split_and_move_pointers': match_pdict_ACtree2.c:1031:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function 'merge_pointers': match_pdict_ACtree2.c:1076:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: At top level: match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pdict_Twobit.c -o match_pdict_Twobit.o match_pdict_Twobit.c: In function 'build_Twobit': match_pdict_Twobit.c:75:27: warning: 'twobit_sign2pos' may be used uninitialized [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~ match_pdict_Twobit.c:110:19: note: 'twobit_sign2pos' was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pdict_utils.c -o match_pdict_utils.o match_pdict_utils.c: In function 'match_ppheadtail0': match_pdict_utils.c:653:56: warning: unused variable 'ncol' [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function 'match_ppheadtail': match_pdict_utils.c:713:13: warning: unused variable 'nelt' [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function '_match_pdict_all_flanks': match_pdict_utils.c:820:51: warning: unused variable 'subtotal_NFC' [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable 'total_NFC' [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable 'NFC' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable 'nloci' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable 'ndup' [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ match_pdict_utils.c: At top level: match_pdict_utils.c:820:34: warning: 'total_NFC' defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:820:51: warning: 'subtotal_NFC' defined but not used [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:261:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_reporting.c -o match_reporting.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchprobes.c -o matchprobes.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatchPattern.c -o pmatchPattern.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_fasta_files.c -o read_fasta_files.o In function 'new_FASTAloaderExt', inlined from 'read_fasta_files' at read_fasta_files.c:430:15: read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' may be used uninitialized [-Wmaybe-uninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function 'read_fasta_files': read_fasta_files.c:182:24: note: 'loader_ext' declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function 'new_FASTAloaderExt', inlined from 'read_fasta_files' at read_fasta_files.c:430:15: read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' may be used uninitialized [-Wmaybe-uninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function 'read_fasta_files': read_fasta_files.c:182:24: note: 'loader_ext' declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function 'new_FASTAloaderExt', inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15: read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' is used uninitialized [-Wuninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function 'read_fasta_blocks': read_fasta_files.c:182:24: note: 'loader_ext' declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ In function 'new_FASTAloaderExt', inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15: read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' is used uninitialized [-Wuninitialized] 186 | return loader_ext; | ^~~~~~~~~~ read_fasta_files.c: In function 'read_fasta_blocks': read_fasta_files.c:182:24: note: 'loader_ext' declared here 182 | FASTAloaderExt loader_ext; | ^~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_fastq_files.c -o read_fastq_files.o read_fastq_files.c: In function 'parse_FASTQ_file': read_fastq_files.c:392:28: warning: 'dont_load' may be used uninitialized [-Wmaybe-uninitialized] 392 | if (dont_load || loader->new_empty_seq_hook == NULL) | ^ read_fastq_files.c:309:26: note: 'dont_load' was declared here 309 | lineinrecno, dont_load; | ^~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replaceAt.c -o replaceAt.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replace_letter_at.c -o replace_letter_at.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strutils.c -o strutils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c translate.c -o translate.o In function 'translate', inlined from 'DNAStringSet_translate' at translate.c:195:4: translate.c:110:36: warning: 'if_ambig0' may be used uninitialized [-Wmaybe-uninitialized] 110 | if (if_ambig == TRANSLATE_ERROR) { | ^ translate.c: In function 'DNAStringSet_translate': translate.c:136:36: note: 'if_ambig0' was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~ In function 'translate', inlined from 'DNAStringSet_translate' at translate.c:195:4: translate.c:106:36: warning: 'if_non_ambig0' may be used uninitialized [-Wmaybe-uninitialized] 106 | if (if_non_ambig == TRANSLATE_TO_X) | ^ translate.c: In function 'DNAStringSet_translate': translate.c:136:21: note: 'if_non_ambig0' was declared here 136 | int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode; | ^~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function '_get_twobit_signature': utils.c:157:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: 'twobit_sign' was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function '_get_twobit_signature_at': utils.c:164:19: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized] 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xscat.c -o xscat.o In file included from F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h: In function 'XString_xscat': F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:91:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~ xscat.c:18:20: note: 'ans_length' was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: 'ans_classname' may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~ xscat.c:20:21: note: 'ans_classname' was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h: In function 'XStringSet_xscat': F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:85:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~ xscat.c:66:39: note: 'ans_length' was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: 'ans_element_type' may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~ xscat.c:68:21: note: 'ans_element_type' was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ 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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs/x64 ** 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 'pattern' 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings)