Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Biostrings package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biostrings.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 190/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Biostrings 2.60.2 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: Biostrings |
Version: 2.60.2 |
Command: rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biostrings.buildbin-libdir Biostrings_2.60.2.tar.gz |
StartedAt: 2021-10-15 08:17:41 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 08:19:16 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 94.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: Biostrings_2.60.2.zip |
PackageFileSize: 14.07 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Biostrings.buildbin-libdir && mkdir Biostrings.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Biostrings.buildbin-libdir Biostrings_2.60.2.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'Biostrings' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BAB_class.c -o BAB_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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] static void BitMatrix_print(BitMatrix *bitmat) ^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable] IntAE *poffsets, *poffsets_order; ^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PreprocessedTB_class.c -o PreprocessedTB_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Biostrings.c -o R_init_Biostrings.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RoSeqs_utils.c -o RoSeqs_utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SparseList_utils.c -o SparseList_utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XStringSetList_class.c -o XStringSetList_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:124:3: warning: 'lkup_len' may be used uninitialized in this function [-Wmaybe-uninitialized] _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INTEGER(start)[i], lkup0, lkup_len); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XString_class.c -o XString_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(ans_elt)[0] = score; ~~~~~~~~~~~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:250:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized] jPattern += indelWidthSubject; ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:231:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:221:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized] int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; ^~~~~~~~~~~~~~~~~ align_utils.c:232:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c find_palindromes.c -o find_palindromes.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtestsim.c -o gtestsim.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inject_code.c -o inject_code.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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] 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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lowlevel_matching.c -o lowlevel_matching.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_PWM.c -o match_PWM.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern.c -o match_pattern.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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] static void test_match_pattern_indels(const char *p, const char *s, ^~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_shiftor.c -o match_pattern_shiftor.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:1031:10: 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; ^~~~~ At top level: 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:75:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); ^~~~~~~~~~~~~~~~~~~~~ match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here SEXP ans, twobit_sign2pos; ^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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: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 ^~~~ At top level: match_pdict_utils.c:819:27: warning: 'total_NFC' defined but not used [-Wunused-variable] static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; ^~~~~~~~~ match_pdict_utils.c:819:44: warning: 'subtotal_NFC' defined but not used [-Wunused-variable] static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; ^~~~~~~~~~~~ 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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_reporting.c -o match_reporting.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchprobes.c -o matchprobes.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatchPattern.c -o pmatchPattern.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_fasta_files.c -o read_fasta_files.o read_fasta_files.c: In function 'read_fasta_files': read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+32)' may be used uninitialized in this function [-Wmaybe-uninitialized] return loader_ext; ^~~~~~~~~~ read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+36)' may be used uninitialized in this function [-Wmaybe-uninitialized] read_fasta_files.c: In function 'read_fasta_blocks': read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+32)' is used uninitialized in this function [-Wuninitialized] return loader_ext; ^~~~~~~~~~ read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+36)' is used uninitialized in this function [-Wuninitialized] "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/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:392:7: warning: 'dont_load' may be used uninitialized in this function [-Wmaybe-uninitialized] if (dont_load || loader->new_empty_seq_hook == NULL) ^ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replaceAt.c -o replaceAt.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replace_letter_at.c -o replace_letter_at.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strutils.c -o strutils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unstrsplit_methods.c -o unstrsplit_methods.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function '_get_twobit_signature': utils.c:157:9: 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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xscat.c -o xscat.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include/Rdefines.h:100:21: 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; ^~~~~~~~~~ xscat.c:52:16: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); ^~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include/Rdefines.h:94:25: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized] #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) ^~~~~~~~~~~~~~ xscat.c:66:32: note: 'ans_length' was declared here int nargs, *arg_lengths, *ii, ans_length, i, j, *width; ^~~~~~~~~~ xscat.c:108:16: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); ^~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Biostrings.buildbin-libdir/00LOCK-Biostrings/00new/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 'pattern' 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 REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/Biostrings.buildbin-libdir/00LOCK-Biostrings/00new/Biostrings/help/InDel.html MIndex-class html MaskedXString-class html MultipleAlignment-class html finding level-2 HTML links ... done PDict-class html PairwiseAlignments-class html PairwiseAlignments-io html QualityScaledXStringSet-class html RNAString-class html XString-class html XStringPartialMatches-class html XStringQuality-class html XStringSet-class html XStringSet-comparison html XStringSet-io html XStringSetList-class html XStringViews-class html align-utils html chartr html detail html dinucleotideFrequencyTest html findPalindromes html getSeq html gregexpr2 html injectHardMask html letter html letterFrequency html longestConsecutive html lowlevel-matching html maskMotif html match-utils html matchLRPatterns html matchPDict-exact html matchPDict-inexact html matchPWM html matchPattern html matchProbePair html matchprobes html misc html needwunsQS html nucleotideFrequency html padAndClip html pairwiseAlignment html phiX174Phage html pid html pmatchPattern html replaceAt html replaceLetterAt html reverseComplement html seqinfo html 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'Biostrings' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c BAB_class.c -o BAB_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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] static void BitMatrix_print(BitMatrix *bitmat) ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable] IntAE *poffsets, *poffsets_order; ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PreprocessedTB_class.c -o PreprocessedTB_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Biostrings.c -o R_init_Biostrings.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RoSeqs_utils.c -o RoSeqs_utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SparseList_utils.c -o SparseList_utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XStringSetList_class.c -o XStringSetList_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:124:3: warning: 'lkup_len' may be used uninitialized in this function [-Wmaybe-uninitialized] _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INTEGER(start)[i], lkup0, lkup_len); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XString_class.c -o XString_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized] INTEGER(ans_elt)[0] = score; ~~~~~~~~~~~~~~~~~~~~^~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:250:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized] jPattern += indelWidthSubject; ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:231:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:221:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized] int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; ^~~~~~~~~~~~~~~~~ align_utils.c:232:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c find_palindromes.c -o find_palindromes.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtestsim.c -o gtestsim.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inject_code.c -o inject_code.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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] 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lowlevel_matching.c -o lowlevel_matching.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_PWM.c -o match_PWM.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern.c -o match_pattern.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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] static void test_match_pattern_indels(const char *p, const char *s, ^~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_pattern_shiftor.c -o match_pattern_shiftor.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:1031:10: 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; ^~~~~ At top level: 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:75:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); ^~~~~~~~~~~~~~~~~~~~~ match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here SEXP ans, twobit_sign2pos; ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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: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 ^~~~ At top level: match_pdict_utils.c:819:27: warning: 'total_NFC' defined but not used [-Wunused-variable] static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; ^~~~~~~~~ match_pdict_utils.c:819:44: warning: 'subtotal_NFC' defined but not used [-Wunused-variable] static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; ^~~~~~~~~~~~ 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c match_reporting.c -o match_reporting.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matchprobes.c -o matchprobes.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatchPattern.c -o pmatchPattern.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_fasta_files.c -o read_fasta_files.o read_fasta_files.c: In function 'read_fasta_files': read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+64)' may be used uninitialized in this function [-Wmaybe-uninitialized] return loader_ext; ^~~~~~~~~~ read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+72)' may be used uninitialized in this function [-Wmaybe-uninitialized] read_fasta_files.c: In function 'read_fasta_blocks': read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+64)' is used uninitialized in this function [-Wuninitialized] return loader_ext; ^~~~~~~~~~ read_fasta_files.c:186:9: warning: '*((void *)&loader_ext+72)' is used uninitialized in this function [-Wuninitialized] "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/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:392:7: warning: 'dont_load' may be used uninitialized in this function [-Wmaybe-uninitialized] if (dont_load || loader->new_empty_seq_hook == NULL) ^ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replaceAt.c -o replaceAt.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c replace_letter_at.c -o replace_letter_at.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c strutils.c -o strutils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unstrsplit_methods.c -o unstrsplit_methods.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o utils.c: In function '_get_twobit_signature': utils.c:157:9: 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xscat.c -o xscat.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include/Rdefines.h:100:21: 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; ^~~~~~~~~~ xscat.c:52:16: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); ^~~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18, from C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include/Rdefines.h:94:25: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized] #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) ^~~~~~~~~~~~~~ xscat.c:66:32: note: 'ans_length' was declared here int nargs, *arg_lengths, *ii, ans_length, i, j, *width; ^~~~~~~~~~ xscat.c:108:16: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized] PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); ^~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Biostrings' as Biostrings_2.60.2.zip * DONE (Biostrings)