##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL dada2
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'dada2' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7,
from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: 'void dada2::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
14 | void validateSignature(const char* sig) {
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:71:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
71 | if(quals.nrow() != maxlen) {
| ~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:316:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
316 | 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::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:288:9: warning: 'k8' may be used uninitialized [-Wmaybe-uninitialized]
288 | free(k8);
| ~~~~^~~~
Rmain.cpp:122:12: note: 'k8' was declared here
122 | uint8_t *k8;
| ^~
Rmain.cpp:289:9: warning: 'k16' may be used uninitialized [-Wmaybe-uninitialized]
289 | free(k16);
| ~~~~^~~~~
Rmain.cpp:123:13: note: 'k16' was declared here
123 | uint16_t *k16;
| ^~~
Rmain.cpp:290:9: warning: 'kord' may be used uninitialized [-Wmaybe-uninitialized]
290 | free(kord);
| ~~~~^~~~~~
Rmain.cpp:124:13: note: 'kord' was declared here
124 | uint16_t *kord;
| ^~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
25 | for(i=0;i<pars.size() && rval==false;i++) {
| ~^~~~~~~~~~~~
chimera.cpp:29:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
29 | if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
| ~~~~~~~~~~~~~^~~~~~~~~~~~
chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
44 | if((max_right+max_left)>=sq.size()) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
48 | 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 of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
48 | 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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
231 | while(al[0][pos] == '-' && pos<len) {
| ~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
237 | while(pos<len && al[0][pos] == al[1][pos]) {
| ~~~^~~~
chimera.cpp:244:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
244 | if(pos<len && al[0][pos] != '-') { left_oo++; }
| ~~~^~~~
chimera.cpp:245:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
245 | while(pos<len && al[0][pos] == al[1][pos]) {
| ~~~^~~~
chimera.cpp:254:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
254 | while(al[1][pos] == '-' && pos>+(len-max_shift)) {
| ~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]
17 | 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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
166 | for(row=0;row<errMat.nrow();row++) {
| ~~~^~~~~~~~~~~~~~
cluster.cpp:167:18: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
167 | for(col=0;col<errMat.ncol();col++) {
| ~~~^~~~~~~~~~~~~~
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
156 | unsigned int index, cind, row, col, ncol;
| ^~~~
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
284 | for(i=0;i<b->nclust;i++) {
| ~^~~~~~~~~~
cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
285 | for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
| ~^~~~~~~~~~~~~~~
cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
288 | if(raw->reads < min_abund) { continue; }
| ~~~~~~~~~~~^~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:141:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
141 | for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
| ~^~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
178 | unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
| ^~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
88 | } 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 of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
133 | for(i=0;i<s1.size();i++) {
| ~^~~~~~~~~~
evaluate.cpp:152:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
152 | for(i=0;i<s1.size();i++) {
| ~^~~~~~~~~~
evaluate.cpp:163:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
163 | for(i=0;i<s1.size();i++) {
| ~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
219 | for(int i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
243 | for(int i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
255 | for(int i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
286 | for(int i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
298 | for(i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
310 | for(j=0;j<klen_min;j++) {
| ~^~~~~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
339 | for(i=0;i<nseqs;i++) {
| ~^~~~~~
evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
348 | for(j=0;j<n_kmers;j++) {
| ~^~~~~~~~
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
327 | size_t len1 = 0, len2 = 0;
| ^~~~
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
327 | size_t len1 = 0, len2 = 0;
| ^~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
16 | for(i=0;i<len;i++) {
| ~^~~~
filter.cpp:20:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
20 | for(i=0;i<seqs.size();i++) {
| ~^~~~~~~~~~~~
filter.cpp:24:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
24 | for(j=0;j<=(len-word_size);j++) {
| ~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
85 | for(i=0;i<STEP;i++) {
| ~^~~~~
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:110:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
110 | for(i=0;i<klen;i++) {
| ~^~~~~
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:141:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
141 | for(i=0;i<STEP;i++) {
| ~^~~~~
kmers.cpp:144:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
144 | 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:162:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
162 | if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
| ~~^~~~~~
kmers.cpp:174:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
174 | for(i=0; i<klen; i++) {
| ~^~~~~
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:211:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
211 | if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
| ~~^~~~~~
kmers.cpp:221:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
221 | for(i=0; i<klen; i++) {
| ~^~~~~
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:250:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
250 | if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
| ~~^~~~~~
kmers.cpp:255:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
255 | for(i=0;i<klen;i++) { kord[i] = 0; }
| ~^~~~~
kmers.cpp:257:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
257 | for(i=0; i<klen; i++) {
| ~^~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
24 | for(int i=0;i<strlen(al0);i++) {
| ~^~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
89 | for (i = 0; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
95 | for (j = 0; j <= len2; j++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
114 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:114:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
114 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:115:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
115 | for(i=0;i<=len1;i++) {
| ~^~~~~~
nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
117 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
| ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:122:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
122 | for (i = 1; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
125 | r = i+rband; if(r>len2) { r = len2; }
| ~^~~~~
nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
130 | if (i == len1) {
| ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
137 | if (j == len2) {
| ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
201 | 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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
230 | for (i=0,j=0;j<len1;j++) {
| ~^~~~~
nwalign_endsfree.cpp:231:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
231 | if (j==len1-1 || s1[j]!=s1[j+1]) {
| ~^~~~~~~~
nwalign_endsfree.cpp:244:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
244 | for (i=0,j=0;j<len2;j++) {
| ~^~~~~
nwalign_endsfree.cpp:245:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
245 | if (j==len2-1 || s2[j]!=s2[j+1]) {
| ~^~~~~~~~
nwalign_endsfree.cpp:264:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
264 | for (i = 0; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
270 | for (j = 0; j <= len2; j++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
289 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:289:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
289 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:290:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
290 | for(i=0;i<=len1;i++) {
| ~^~~~~~
nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
292 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
| ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:297:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
297 | for (i = 1; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
300 | r = i+rband; if(r>len2) { r = len2; }
| ~^~~~~
nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
305 | if (i == len1) {
| ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
314 | if (j == len2) {
| ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
379 | 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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
419 | for (i = 1; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
425 | for (j = 1; j <= len2; j++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
444 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:444:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
444 | if(band>=0 && (band<len1 || band<len2)) {
| ~~~~^~~~~
nwalign_endsfree.cpp:445:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
445 | for(i=0;i<=len1;i++) {
| ~^~~~~~
nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
447 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
| ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:452:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
452 | for (i = 1; i <= len1; i++) {
| ~~^~~~~~~
nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
455 | r = i+rband; if(r>len2) { r = len2; }
| ~^~~~~
nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
522 | 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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
548 | for (int i=0;i<len_al;i++) {
| ~^~~~~~~
nwalign_endsfree.cpp:549:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
549 | al[0][i] = i < len1 ? s1[i] : '-';
| ~~^~~~~~
nwalign_endsfree.cpp:550:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
550 | 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 of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
658 | for(s=0;s<sub->nsubs;s++) {
| ~^~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
96 | start_col = 1 + (1+(band<len1 ? band : len1))/2;
| ~~~~^~~~~
nwalign_vectorized.cpp:125:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
125 | while(row < (1 + (band < len1 ? band : len1))) {
| ~~~~~^~~~~~
nwalign_vectorized.cpp:178:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
178 | if(row==(band<len1 ? band : len1)) {
| ~~~~^~~~~
nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
218 | if(row < band && row < len1) { // upper tri for seq1
| ~~~~^~~~~~
nwalign_vectorized.cpp:280:27: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:31: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:47: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:59: warning: format '%i' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:62: warning: format '%i' expects argument of type 'int', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:71: warning: format '%i' expects argument of type 'int', but argument 8 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:280:74: warning: format '%i' expects argument of type 'int', but argument 9 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
280 | Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
| ~^ ~~~~~~~~~~~~~~~~~~~
| | |
| int size_t {aka long long unsigned int}
| %lli
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
75 | size_t start_col, end_col;
| ^~~~~~~
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
330 | for(i=0;i<s1.size();i++) {
| ~^~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
121 | for(s=0;s<sub->nsubs;s++) {
| ~^~~~~~~~~~~
pval.cpp:123:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
123 | 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 of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
177 | for(s=0;s<sub->nsubs;s++) {
| ~^~~~~~~~~~~
pval.cpp:179:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
179 | if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
| ~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:48:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
48 | if(kmer>=0 && kmer<n_kmers) {
| ~~~~^~~~~~~~
taxonomy.cpp: In function 'int get_best_genus(int*, float*, unsigned int, unsigned int, unsigned int, float*)':
taxonomy.cpp:84:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
84 | for(g=0;g<ngenus;g++) {
| ~^~~~~~~
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
145 | unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
| ^~~~~~~~~~
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:222:45: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
222 | if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:252:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
252 | for(kmer=0;kmer<n_kmers;kmer++) {
| ~~~~^~~~~~~~
taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
261 | for(kmer=0;kmer<n_kmers;kmer++) {
| ~~~~^~~~~~~~
taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
268 | for(kmer=0;kmer<n_kmers;kmer++) {
| ~~~~^~~~~~~~
taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
287 | for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
| ~^~~~~~~~~~~~~
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 -LF:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-dada2/00new/dada2/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dada2)
