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###
### Running command:
###
### rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.22.0.tar.gz
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install for i386
* installing *source* package 'dada2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
void validateSignature(const char* sig) {
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
if(quals.nrow() != maxlen) {
~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp:82:8: 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, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:313:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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::__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:287:9: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(kord);
~~~~^~~~~~
Rmain.cpp:286:9: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k16);
~~~~^~~~~
Rmain.cpp:285:9: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k8);
~~~~^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::__cxx11::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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
while(al[0][pos] == '-' && pos<len) {
~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
while(al[1][pos] == '-' && pos>+(len-max_shift)) {
~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
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]
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]
if(raw->reads < min_abund) { continue; }
~~~~~~~~~~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::string)':
evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
} while((s1gap || s2gap) && start<s1.size());
~~~~~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::__cxx11::string, std::__cxx11::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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
~^~~~~~
evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(int i=0;i<nseqs;i++) {
~^~~~~~
evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(i=0;i<nseqs;i++) {
~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(i=0;i<nseqs;i++) {
~^~~~~~
evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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::__cxx11::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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]
for(j=0;j<=(len-word_size);j++) {
~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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:81:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(i=0;i<STEP;i++) {
~^~~~~
kmers.cpp:134:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:158:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:205:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:239:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(i=0;i<klen;i++) { kord[i] = 0; }
~^~~~~
kmers.cpp:241:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(i=0; i<klen; i++) {
~^~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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 'unsigned int'} [-Wsign-compare]
for(int i=0;i<strlen(al0);i++) {
~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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 'unsigned int'} [-Wsign-compare]
for (i = 0; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (j = 0; j <= len2; j++) {
~~^~~~~~~
nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(i=0;i<=len1;i++) {
~^~~~~~
nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for (i = 1; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
if (i == len1) {
~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (j == len2) {
~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for (i = 0; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (j = 0; j <= len2; j++) {
~~^~~~~~~
nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(i=0;i<=len1;i++) {
~^~~~~~
nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for (i = 1; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
if (i == len1) {
~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (j == len2) {
~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (i = 1; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for (j = 1; j <= len2; j++) {
~~^~~~~~~
nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(i=0;i<=len1;i++) {
~^~~~~~
nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for (i = 1; i <= len1; i++) {
~~^~~~~~~
nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
for(s=0;s<sub->nsubs;s++) {
~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
if(row==(band<len1 ? band : len1)) {
~~~~^~~~~
nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-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::__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 'unsigned int'} [-Wsign-compare]
for(i=0;i<s1.size();i++) {
~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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 'unsigned int'} [-Wsign-compare]
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]
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]
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 'unsigned int'} [-Wsign-compare]
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 'unsigned int'} [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
~~~~^~~~~~~~
taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
~~~~^~~~~~~~
taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
for(kmer=0;kmer<n_kmers;kmer++) {
~~~~^~~~~~~~
taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
~^~~~~~~~~~~~~
C:/rtools40/mingw32/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-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/dada2.buildbin-libdir/00LOCK-dada2/00new/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
derep-class html
derepFasta html
derepFastq html
errBalancedF html
errBalancedR html
fastqFilter html
fastqPairedFilter html
filterAndTrim html
getDadaOpt html
getErrors html
getSequences html
getUniques html
inflateErr html
isBimera html
isBimeraDenovo html
isBimeraDenovoTable html
isPhiX html
isShiftDenovo html
learnErrors html
loessErrfun html
makeSequenceTable html
makeSpeciesFasta_RDP html
makeSpeciesFasta_Silva html
makeTaxonomyFasta_RDP html
makeTaxonomyFasta_Silva html
makeTaxonomyFasta_SilvaNR html
mergePairs html
mergeSequenceTables html
names-set-dada-ANY-method html
names-set-derep-ANY-method html
noqualErrfun html
nwalign html
nwhamming html
plotComplexity html
plotErrors html
plotQualityProfile html
qtables2 html
rc html
removeBimeraDenovo html
removePrimers html
seqComplexity html
setDadaOpt html
show-methods html
tperr1 html
uniques-vector html
uniquesToFasta html
writeFasta html
** 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
install for x64
* installing *source* package 'dada2' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
void validateSignature(const char* sig) {
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
if(quals.nrow() != maxlen) {
~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp:82:8: 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, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:313:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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::__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:287:9: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(kord);
~~~~^~~~~~
Rmain.cpp:286:9: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k16);
~~~~^~~~~
Rmain.cpp:285:9: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(k8);
~~~~^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::__cxx11::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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
while(al[1][pos] == '-' && pos>+(len-max_shift)) {
~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
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]
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]
if(raw->reads < min_abund) { continue; }
~~~~~~~~~~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -msse2 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::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]
} while((s1gap || s2gap) && start<s1.size());
~~~~~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::__cxx11::string, std::__cxx11::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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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::__cxx11::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
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]
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]
for(j=0;j<=(len-word_size);j++) {
~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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:81:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(i=0;i<STEP;i++) {
~^~~~~
kmers.cpp:134:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:158:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:205:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
~~^~~~~~
kmers.cpp:239:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(i=0;i<klen;i++) { kord[i] = 0; }
~^~~~~
kmers.cpp:241:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
for(i=0; i<klen; i++) {
~^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
for(int i=0;i<strlen(al0);i++) {
~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
for(s=0;s<sub->nsubs;s++) {
~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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]
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::__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]
for(i=0;i<s1.size();i++) {
~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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]
if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/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]
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]
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]
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]
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]
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]
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]
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]
for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
~^~~~~~~~~~~~~
C:/rtools40/mingw64/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-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.22.0.zip
* DONE (dada2)
