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###
### Running command:
###
### rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.12.1.tar.gz
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install for i386
* installing *source* package 'dada2' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7:0,
from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: 'void dada2::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
void validateSignature(const char* sig) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:68:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(quals.nrow() != maxlen) {
^
Rmain.cpp:81:8: warning: variable 'HW_SSE3' set but not used [-Wunused-but-set-variable]
bool HW_SSE3 = false;
^
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
^
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:282:15: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(kord);
^
Rmain.cpp:281:14: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k16);
^
Rmain.cpp:280:13: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k8);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
^
chimera.cpp:44:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((max_right+max_left)>=sq.size()) {
^
chimera.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
^
chimera.cpp:48:83: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
^
chimera.cpp: In function 'void get_lr(char**, int&, int&, int&, int&, bool, int)':
chimera.cpp:231:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(al[0][pos] == '-' && pos+(len-max_shift)) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:17:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
unsigned int index, cind, center_reads;
^
cluster.cpp: In function 'void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:166:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(row=0;rownclust;i++) {
^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=1; rbi[i]->nraw; r++) { // r=0 is the center
^
cluster.cpp:321:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(raw->reads < min_abund) { continue; }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;inclust;i++) { bi_free(b->bi[i]); }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c error.cpp -o error.o
error.cpp: In function 'Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)':
error.cpp:170:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
} while((s1gap || s2gap) && start >, std::vector >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:158:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:205:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:239:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:130:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:137:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:305:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:314:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:379:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;insubs;s++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
start_col = 1 + (1+(band >, std::vector >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;insubs;s++) {
^
pval.cpp:123:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
^
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:177:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;snsubs;s++) {
^
pval.cpp:179:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:42:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(kmer>=0 && kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:120:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:149:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:345:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:374:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:68:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(quals.nrow() != maxlen) {
^
Rmain.cpp:81:8: warning: variable 'HW_SSE3' set but not used [-Wunused-but-set-variable]
bool HW_SSE3 = false;
^
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
^
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:282:15: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(kord);
^
Rmain.cpp:281:14: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k16);
^
Rmain.cpp:280:13: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k8);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
^
chimera.cpp:44:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((max_right+max_left)>=sq.size()) {
^
chimera.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
^
chimera.cpp:48:83: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
^
chimera.cpp: In function 'void get_lr(char**, int&, int&, int&, int&, bool, int)':
chimera.cpp:231:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(al[0][pos] == '-' && pos+(len-max_shift)) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:17:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
unsigned int index, cind, center_reads;
^
cluster.cpp: In function 'void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:166:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(row=0;rownclust;i++) {
^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=1; rbi[i]->nraw; r++) { // r=0 is the center
^
cluster.cpp:321:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(raw->reads < min_abund) { continue; }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;inclust;i++) { bi_free(b->bi[i]); }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c error.cpp -o error.o
error.cpp: In function 'Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)':
error.cpp:170:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
} while((s1gap || s2gap) && start >, std::vector >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i >, std::vector >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:158:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:205:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
^
kmers.cpp:239:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:130:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:137:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:305:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:314:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:379:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i=0 && (band=0 && (bandlen2) { r = len2; }
^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;insubs;s++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
start_col = 1 + (1+(band >, std::vector >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;insubs;s++) {
^
pval.cpp:123:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
^
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:177:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;snsubs;s++) {
^
pval.cpp:179:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:42:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(kmer>=0 && kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:120:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:149:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer >, std::vector >, std::vector >, std::vector, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:345:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:374:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer
