install for i386
* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, bool, double, int, double, int, double, int, bool, int, bool, bool, int, bool)':
Rmain.cpp:56:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(quals.nrow() != seqlen) {
^
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int (*)[4], int, int, bool, double, int, double, int, double, int, bool, int, bool, bool, bool)':
Rmain.cpp:164:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, verbose)) ) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::basic_string<char> >, bool, int, Rcpp::NumericMatrix, int, int)':
chimera.cpp:30:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size();i++) {
^
chimera.cpp:43:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size() && rval==false;i++) {
^
chimera.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
^
chimera.cpp:103:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((max_right+max_left)>=sq.size()) {
^
chimera.cpp:107:39: 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:107:83: 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:17:35: warning: 'right_oo' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, left, right, left_oo, right_oo, pos, len, max_len;
^
chimera.cpp:17:26: warning: 'left_oo' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, left, right, left_oo, right_oo, pos, len, max_len;
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_free(B*)':
cluster.cpp:160:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
^
cluster.cpp: In function 'int b_bud(B*, double, int, bool)':
cluster.cpp:403:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<b->nclust;i++) {
^
cluster.cpp:404:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=0; r<b->bi[i]->nraw; r++) {
^
cluster.cpp:414:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
((raw->p == minp && raw->reads > minreads))) { // Most significant
^
cluster.cpp:435:29: warning: 'mine' may be used uninitialized in this function [-Wmaybe-uninitialized]
b->bi[i]->birth_e = mine;
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:154:51: 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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:87:36: 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)':
evaluate.cpp:132:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:151:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp: In function 'Rcpp::DataFrame evaluate_kmers(std::vector<std::basic_string<char> >, int, Rcpp::NumericMatrix, int, int, unsigned int)':
evaluate.cpp:235:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(max_aligns < (nseqs * (nseqs-1)/2)) { // More potential comparisons than max
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:17:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<len;i++) {
^
filter.cpp:21:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<seqs.size();i++) {
^
filter.cpp:25:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<=(len-word_size);j++) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:103:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:109:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:128:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:129:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:131:20: 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:136:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:139:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:144:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:151:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:215:13: 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*, const char*, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:246:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len1;j++) {
^
nwalign_endsfree.cpp:247:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len1-1 || s1[j]!=s1[j+1]) {
^
nwalign_endsfree.cpp:260:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len2;j++) {
^
nwalign_endsfree.cpp:261:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len2-1 || s2[j]!=s2[j+1]) {
^
nwalign_endsfree.cpp:280:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:286:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:305:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:305:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:306:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:308:20: 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:313:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:316:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:321:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:330:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:395:13: 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*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:435:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:441:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 1; j <= len2; j++) {
^
nwalign_endsfree.cpp:460:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:460:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:461:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:463:20: 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:468:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:471:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:538:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int (*)[4], int, int, bool, double, int, bool)':
nwalign_endsfree.cpp:672:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_endsfree_vectorized(char*, char*, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:51:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band<0 || band>len1) {
^
nwalign_vectorized.cpp:71:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row<band+1) {
^
nwalign_vectorized.cpp:83:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row<band+1) {
^
nwalign_vectorized.cpp:124:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row <= band) {
^
nwalign_vectorized.cpp:136:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(++row > band) break;
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:93:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c strmap.cpp -o strmap.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:41:23: 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*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:65:12: 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<int>, Rcpp::IntegerMatrix, bool)':
taxonomy.cpp:112:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:150:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<(genusmat.ncol());i++) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/dada2.buildbin-libdir/dada2/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, bool, double, int, double, int, double, int, bool, int, bool, bool, int, bool)':
Rmain.cpp:56:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(quals.nrow() != seqlen) {
^
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int (*)[4], int, int, bool, double, int, double, int, double, int, bool, int, bool, bool, bool)':
Rmain.cpp:164:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, verbose)) ) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::basic_string<char> >, bool, int, Rcpp::NumericMatrix, int, int)':
chimera.cpp:30:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size();i++) {
^
chimera.cpp:43:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<pars.size() && rval==false;i++) {
^
chimera.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
^
chimera.cpp:103:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if((max_right+max_left)>=sq.size()) {
^
chimera.cpp:107:39: 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:107:83: 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:17:35: warning: 'right_oo' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, left, right, left_oo, right_oo, pos, len, max_len;
^
chimera.cpp:17:26: warning: 'left_oo' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, left, right, left_oo, right_oo, pos, len, max_len;
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_free(B*)':
cluster.cpp:160:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
^
cluster.cpp: In function 'int b_bud(B*, double, int, bool)':
cluster.cpp:403:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<b->nclust;i++) {
^
cluster.cpp:404:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(r=0; r<b->bi[i]->nraw; r++) {
^
cluster.cpp:414:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
((raw->p == minp && raw->reads > minreads))) { // Most significant
^
cluster.cpp:435:29: warning: 'mine' may be used uninitialized in this function [-Wmaybe-uninitialized]
b->bi[i]->birth_e = mine;
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:154:51: 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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:87:36: 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)':
evaluate.cpp:132:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp:151:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<s1.size();i++) {
^
evaluate.cpp: In function 'Rcpp::DataFrame evaluate_kmers(std::vector<std::basic_string<char> >, int, Rcpp::NumericMatrix, int, int, unsigned int)':
evaluate.cpp:235:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(max_aligns < (nseqs * (nseqs-1)/2)) { // More potential comparisons than max
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:17:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<len;i++) {
^
filter.cpp:21:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<seqs.size();i++) {
^
filter.cpp:25:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(j=0;j<=(len-word_size);j++) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:103:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:109:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:128:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:128:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:129:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:131:20: 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:136:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:139:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:144:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:151:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:215:13: 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*, const char*, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:246:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len1;j++) {
^
nwalign_endsfree.cpp:247:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len1-1 || s1[j]!=s1[j+1]) {
^
nwalign_endsfree.cpp:260:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0,j=0;j<len2;j++) {
^
nwalign_endsfree.cpp:261:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j==len2-1 || s2[j]!=s2[j+1]) {
^
nwalign_endsfree.cpp:280:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i <= len1; i++) {
^
nwalign_endsfree.cpp:286:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j <= len2; j++) {
^
nwalign_endsfree.cpp:305:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:305:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:306:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:308:20: 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:313:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:316:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:321:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i == len1) {
^
nwalign_endsfree.cpp:330:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (j == len2) {
^
nwalign_endsfree.cpp:395:13: 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*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:435:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:441:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 1; j <= len2; j++) {
^
nwalign_endsfree.cpp:460:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:460:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band>=0 && (band<len1 || band<len2)) {
^
nwalign_endsfree.cpp:461:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<=len1;i++) {
^
nwalign_endsfree.cpp:463:20: 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:468:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i <= len1; i++) {
^
nwalign_endsfree.cpp:471:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
r = i+rband; if(r>len2) { r = len2; }
^
nwalign_endsfree.cpp:538:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i=0;i<len_al;i++) {
^
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int (*)[4], int, int, bool, double, int, bool)':
nwalign_endsfree.cpp:672:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_endsfree_vectorized(char*, char*, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:51:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(band<0 || band>len1) {
^
nwalign_vectorized.cpp:71:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row<band+1) {
^
nwalign_vectorized.cpp:83:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row<band+1) {
^
nwalign_vectorized.cpp:124:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(row <= band) {
^
nwalign_vectorized.cpp:136:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(++row > band) break;
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:93:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c strmap.cpp -o strmap.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:41:23: 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*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:65:12: 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<int>, Rcpp::IntegerMatrix, bool)':
taxonomy.cpp:112:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
^
taxonomy.cpp:141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:150:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
^
taxonomy.cpp:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i<(genusmat.ncol());i++) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.0.3.zip
* DONE (dada2)