Benjamin Callahan
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/dada2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: b8a796b |
| git_last_commit_date: 2021-05-19 12:18:16 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the dada2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dada2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 437/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dada2 1.20.0 (landing page) Benjamin Callahan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: dada2 |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dada2_1.20.0.tar.gz |
| StartedAt: 2021-10-14 21:52:58 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:59:39 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 400.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dada2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dada2_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/dada2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dada2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dada2' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'dada2' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
libs 2.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'C_isACGT' 'matchGenera'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
tax.check: warning in assignTaxonomy(sq.test, fn.tax, multi = TRUE):
partial argument match of 'multi' to 'multithread'
plotComplexity: no visible binding for global variable 'complexity'
plotErrors: no visible binding for global variable 'Qual'
plotErrors: no visible binding for global variable 'Observed'
plotErrors: no visible binding for global variable 'Input'
plotErrors: no visible binding for global variable 'Estimated'
plotErrors: no visible binding for global variable 'Nominal'
plotQualityProfile: no visible binding for global variable 'Cycle'
plotQualityProfile: no visible binding for global variable 'Score'
plotQualityProfile: no visible binding for global variable 'Count'
plotQualityProfile: no visible binding for global variable 'Mean'
plotQualityProfile: no visible binding for global variable 'Q25'
plotQualityProfile: no visible binding for global variable 'Q50'
plotQualityProfile: no visible binding for global variable 'Q75'
plotQualityProfile: no visible binding for global variable 'Cum'
tax.check: no visible binding for global variable 'fn.spc'
Undefined global functions or variables:
Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
Qual Score complexity fn.spc
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
PKG_CFLAGS set in 'src/Makevars.win' without any corresponding files
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/dada2/libs/i386/dada2.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/dada2/libs/x64/dada2.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PacBioErrfun 10.6 0.10 10.79
learnErrors 8.4 0.58 5.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
learnErrors 7.72 0.7 4.86
PacBioErrfun 8.38 0.0 8.55
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 9 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/dada2.Rcheck/00check.log'
for details.
dada2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/dada2_1.20.0.tar.gz && rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL dada2_1.20.0.zip && rm dada2_1.20.0.tar.gz dada2_1.20.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
52 2208k 52 1158k 0 0 1682k 0 0:00:01 --:--:-- 0:00:01 1681k
100 2208k 100 2208k 0 0 2082k 0 0:00:01 0:00:01 --:--:-- 2085k
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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.20.0.zip
* DONE (dada2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'dada2' successfully unpacked and MD5 sums checked
|
dada2.Rcheck/examples_i386/dada2-Ex.timings
|
dada2.Rcheck/examples_x64/dada2-Ex.timings
|