Biostrings 2.38.0
H. Pages
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Biostrings | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL Biostrings
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:193:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
IntAE *poffsets, *poffsets_order;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:123:32: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
_copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function ‘parse_FASTQ_file’:
XStringSet_io.c:812:7: warning: ‘load_rec’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (load_rec && loader->load_qual != NULL)
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XString_class.c -o XString_class.o
XString_class.c: In function ‘new_XString_from_CHARACTER’:
XString_class.c:184:31: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
_copy_CHARSXP_to_Chars_holder(&ans_holder, x_elt,
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:173:22: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(ans_elt)[0] = score;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -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)) {
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -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;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_BOC.c -o match_BOC.o
match_BOC.c: In function ‘BOC_exact_search’:
match_BOC.c:331:3: warning: label ‘continue0’ defined but not used [-Wunused-label]
continue0: ;
^
match_BOC.c:268:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
match_BOC.c:268:59: warning: unused variable ‘offsets’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
match_BOC.c:268:55: warning: unused variable ‘j’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function ‘BOC2_exact_search’:
match_BOC2.c:288:3: warning: label ‘continue0’ defined but not used [-Wunused-label]
continue0: ;
^
match_BOC2.c:234:68: warning: unused variable ‘noffsets’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
match_BOC2.c:234:59: warning: unused variable ‘offsets’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
match_BOC2.c:234:55: warning: unused variable ‘j’ [-Wunused-variable]
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:442:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ans_col += tb_length;
^
match_pdict.c:415:58: 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:493:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ans_elt += P_length;
^
match_pdict.c:464:57: note: ‘ans_elt’ was declared here
int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1069:10: 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:1114:10: 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:640:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:29:0,
from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.2-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’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rinternals.h:652:30: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define PROTECT(s) Rf_protect(s)
^
match_pdict_Twobit.c:126:12: note: ‘twobit_sign2pos’ was declared here
SEXP ans, twobit_sign2pos;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:674:49: 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:734:6: 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:841:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
^
match_pdict_utils.c:841:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
^
match_pdict_utils.c:840:33: warning: unused variable ‘NFC’ [-Wunused-variable]
unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
^
match_pdict_utils.c:840:26: warning: unused variable ‘nloci’ [-Wunused-variable]
unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
^
match_pdict_utils.c:840:20: 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:282:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
static void match_headtail_by_loc(const HeadTail *headtail,
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c strutils.c -o strutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:101:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (if_ambig == TRANSLATE_ERROR) {
^
translate.c:126:29: note: ‘if_ambig0’ was declared here
int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
^
translate.c:97:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (if_non_ambig == TRANSLATE_TO_X)
^
translate.c:126:14: note: ‘if_non_ambig0’ was declared here
int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:210:2: 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:217:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, twobit_sign;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -fpic -g -O2 -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
from /home/biocbuild/bbs-3.2-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’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:78:32: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define NEW_RAW(n) allocVector(RAWSXP,n)
^
xscat.c:18:13: note: ‘ans_length’ was declared here
int nargs, ans_length, tag_offset, j;
^
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:29:0,
from /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
from /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from ../inst/include/Biostrings_defines.h:18,
from Biostrings.h:1,
from xscat.c:1:
/home/biocbuild/bbs-3.2-bioc/R/include/Rinternals.h:652:30: 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 /home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
from /home/biocbuild/bbs-3.2-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’:
/home/biocbuild/bbs-3.2-bioc/R/include/Rdefines.h:72:36: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define NEW_INTEGER(n) allocVector(INTSXP,n)
^
xscat.c:66:32: note: ‘ans_length’ was declared here
int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.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 replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘setequal’ from package ‘base’ 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biostrings)