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###
### Running command:
###
### rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.10.1.tar.gz
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install for i386
* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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::basic_string<char> >, std::vector<int>, std::vector<bool>, 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::basic_string<char> >, std::vector<int>, std::vector<bool>, 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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<std::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size() && rval==false;i++) {
^
chimera.cpp:29:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((left+right) >= 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) {
^
chimera.cpp:237:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(pos<len && al[0][pos] == al[1][pos]) {
^
chimera.cpp:244:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos<len && al[0][pos] != '-') { left_oo++; }
^
chimera.cpp:245:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(pos<len && al[0][pos] == al[1][pos]) {
^
chimera.cpp:254:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(al[1][pos] == '-' && pos>+(len-max_shift)) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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;row<errMat.nrow();row++) {
^
cluster.cpp:167:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(col=0;col<errMat.ncol();col++) {
^
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
unsigned int index, cind, row, col, ncol;
^
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:317:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<b->nclust;i++) {
^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=1; r<b->bi[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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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;i<b->nclust;i++) { bi_free(b->bi[i]); }
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<s1.size());
^
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::string, std::string, int, bool)':
evaluate.cpp:133:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:152:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:163:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp:255:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp:298:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<nseqs;i++) {
^
evaluate.cpp:310:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<klen_min;j++) {
^
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<nseqs;i++) {
^
evaluate.cpp:348:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<n_kmers;j++) {
^
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::basic_string<char> >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<len;i++) {
^
filter.cpp:20:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<seqs.size();i++) {
^
filter.cpp:24:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<=(len-word_size);j++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:81:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<STEP;i++) {
^
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:101:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<klen;i++) {
^
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:131:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<STEP;i++) {
^
kmers.cpp:134:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
^
kmers.cpp: In function 'void assign_kmer8(uint8_t*, const char*, int)':
kmers.cpp:146:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen; i++) {
^
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:195:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen; i++) {
^
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:234:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen;i++) { kord[i] = 0; }
^
kmers.cpp:241:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i<klen; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<strlen(al0);i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:89:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:95:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:114:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:114:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:115:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:117:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:122:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:125:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { 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<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:230:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len1;j++) {
^
nwalign_endsfree.cpp:231:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len1-1 || s1[j]!=s1[j+1]) {
^
nwalign_endsfree.cpp:244:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len2;j++) {
^
nwalign_endsfree.cpp:245:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len2-1 || s2[j]!=s2[j+1]) {
^
nwalign_endsfree.cpp:264:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:270:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:289:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:290:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:297:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:300:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { 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<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:419:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:425:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 1; j <= len2; j++) {
^
nwalign_endsfree.cpp:444:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:444:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:445:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:447:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:452:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:455:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign_gapless(const char*, size_t, const char*, size_t)':
nwalign_endsfree.cpp:548:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp:549:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
al[0][i] = i < len1 ? s1[i] : '-';
^
nwalign_endsfree.cpp:550:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
al[1][i] = i < len2 ? s2[i] : '-';
^
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)':
nwalign_endsfree.cpp:658:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<len1 ? band : len1))/2;
^
nwalign_vectorized.cpp:125:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row < (1 + (band < len1 ? band : len1))) {
^
nwalign_vectorized.cpp:178:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(row==(band<len1 ? band : len1)) {
^
nwalign_vectorized.cpp:218:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(row < band && row < len1) { // upper tri for seq1
^
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
size_t start_col, end_col;
^
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, 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;i<s1.size();i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:121:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;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;s<sub->nsubs;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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<n_kmers) {
^
taxonomy.cpp: In function 'int get_best_genus(int*, double*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:72:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(g=0;g<ngenus;g++) {
^
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, 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<n_kmers;kmer++) {
^
taxonomy.cpp:158:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:223:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<(genusmat.ncol());i++) {
^
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:277:15: warning: variable 'seqlen' set but not used [-Wunused-but-set-variable]
size_t i, seqlen;
^
taxonomy.cpp:278:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
^
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, 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<n_kmers;kmer++) {
^
taxonomy.cpp:383:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:407:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.buildbin-libdir/dada2/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'dada2'
finding HTML links ... done
PacBioErrfun html
addSpecies html
finding level-2 HTML links ... done
assignSpecies html
assignTaxonomy html
c-dada-method html
c-derep-method html
collapseNoMismatch html
dada-class html
dada html
dada2-package html
dada_to_seq_table html
derep-class html
derepFasta html
derepFastq html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/derepFastq.Rd:30: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/derepFastq.Rd:12: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/derepFastq.Rd:19: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
errBalancedF html
errBalancedR html
errExtremeF html
errExtremeR html
errHmpF html
errHmpR html
fastqFilter html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/fastqFilter.Rd:68: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/fastqFilter.Rd:97: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
fastqPairedFilter html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/fastqPairedFilter.Rd:98: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/fastqPairedFilter.Rd:132: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
filterAndTrim html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/filterAndTrim.Rd:101: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/filterAndTrim.Rd:102: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/filterAndTrim.Rd:151: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
getDadaOpt html
getErrors html
getSequences html
getUniques html
inflateErr html
isBimera html
isBimeraDenovo html
isBimeraDenovoTable html
isPhiX html
isShiftDenovo html
learnErrors html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/learnErrors.Rd:14: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
loessErrfun html
makeSequenceTable html
makeSpeciesFasta_RDP html
makeSpeciesFasta_Silva html
makeTaxonomyFasta_RDP html
makeTaxonomyFasta_Silva html
mergePairs html
mergePairsByID html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/mergePairsByID.Rd:54: file link 'id' in package 'ShortRead' does not exist and so has been treated as a topic
mergeSequenceTables html
names-set-dada-ANY-method html
names-set-derep-ANY-method html
noqualErrfun html
nwalign html
nwhamming html
plotErrors html
plotQualityProfile html
qtables2 html
removeBimeraDenovo html
seqComplexity html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/seqComplexity.Rd:52: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
setDadaOpt html
show-methods html
tperr1 html
uniques-vector html
uniquesToFasta html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/uniquesToFasta.Rd:22: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/uniquesToFasta.Rd:27: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/uniquesToFasta.Rd:29: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
writeFasta html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/writeFasta.Rd:21: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YmL7o/R.INSTALL179045dd752f/dada2/man/writeFasta.Rd:31: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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::basic_string<char> >, std::vector<int>, std::vector<bool>, 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::basic_string<char> >, std::vector<int>, std::vector<bool>, 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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<std::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size() && rval==false;i++) {
^
chimera.cpp:29:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((left+right) >= 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) {
^
chimera.cpp:237:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(pos<len && al[0][pos] == al[1][pos]) {
^
chimera.cpp:244:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(pos<len && al[0][pos] != '-') { left_oo++; }
^
chimera.cpp:245:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(pos<len && al[0][pos] == al[1][pos]) {
^
chimera.cpp:254:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(al[1][pos] == '-' && pos>+(len-max_shift)) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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;row<errMat.nrow();row++) {
^
cluster.cpp:167:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(col=0;col<errMat.ncol();col++) {
^
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
unsigned int index, cind, row, col, ncol;
^
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:317:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<b->nclust;i++) {
^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=1; r<b->bi[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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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;i<b->nclust;i++) { bi_free(b->bi[i]); }
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<s1.size());
^
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::string, std::string, int, bool)':
evaluate.cpp:133:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:152:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:163:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp:255:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
^
evaluate.cpp:298:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<nseqs;i++) {
^
evaluate.cpp:310:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<klen_min;j++) {
^
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<nseqs;i++) {
^
evaluate.cpp:348:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<n_kmers;j++) {
^
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
size_t len1 = 0, len2 = 0;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::basic_string<char> >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<len;i++) {
^
filter.cpp:20:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<seqs.size();i++) {
^
filter.cpp:24:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<=(len-word_size);j++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:81:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<STEP;i++) {
^
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:101:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<klen;i++) {
^
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:131:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<STEP;i++) {
^
kmers.cpp:134:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
^
kmers.cpp: In function 'void assign_kmer8(uint8_t*, const char*, int)':
kmers.cpp:146:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen; i++) {
^
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:195:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen; i++) {
^
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:234:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k >= 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<klen;i++) { kord[i] = 0; }
^
kmers.cpp:241:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0; i<klen; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<strlen(al0);i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:89:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:95:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:114:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:114:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:115:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:117:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:122:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:125:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { 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<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:230:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len1;j++) {
^
nwalign_endsfree.cpp:231:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len1-1 || s1[j]!=s1[j+1]) {
^
nwalign_endsfree.cpp:244:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len2;j++) {
^
nwalign_endsfree.cpp:245:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len2-1 || s2[j]!=s2[j+1]) {
^
nwalign_endsfree.cpp:264:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:270:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:289:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:290:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:297:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:300:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { 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<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:419:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:425:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 1; j <= len2; j++) {
^
nwalign_endsfree.cpp:444:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:444:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:445:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:447:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
^
nwalign_endsfree.cpp:452:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:455:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'char** nwalign_gapless(const char*, size_t, const char*, size_t)':
nwalign_endsfree.cpp:548:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp:549:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
al[0][i] = i < len1 ? s1[i] : '-';
^
nwalign_endsfree.cpp:550:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
al[1][i] = i < len2 ? s2[i] : '-';
^
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)':
nwalign_endsfree.cpp:658:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<len1 ? band : len1))/2;
^
nwalign_vectorized.cpp:125:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row < (1 + (band < len1 ? band : len1))) {
^
nwalign_vectorized.cpp:178:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(row==(band<len1 ? band : len1)) {
^
nwalign_vectorized.cpp:218:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(row < band && row < len1) { // upper tri for seq1
^
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
size_t start_col, end_col;
^
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, 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;i<s1.size();i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/extsoft/include" -msse2 -O2 -Wall -mtune=generic -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:121:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;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;s<sub->nsubs;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˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-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<n_kmers) {
^
taxonomy.cpp: In function 'int get_best_genus(int*, double*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:72:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(g=0;g<ngenus;g++) {
^
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, 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<n_kmers;kmer++) {
^
taxonomy.cpp:158:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:223:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<(genusmat.ncol());i++) {
^
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:277:15: warning: variable 'seqlen' set but not used [-Wunused-but-set-variable]
size_t i, seqlen;
^
taxonomy.cpp:278:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
^
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, 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<n_kmers;kmer++) {
^
taxonomy.cpp:383:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:407:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.10.1.zip
* DONE (dada2)
In R CMD INSTALL
In R CMD INSTALL