Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:35:53 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 495/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dada2 1.30.0 (landing page) Benjamin Callahan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the dada2 package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: dada2 |
Version: 1.30.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings dada2_1.30.0.tar.gz |
StartedAt: 2024-04-15 21:48:59 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-15 21:54:08 -0400 (Mon, 15 Apr 2024) |
EllapsedTime: 309.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dada2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings dada2_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/dada2.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘dada2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dada2’ version ‘1.30.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘dada2’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: extdata 2.1Mb libs 7.5Mb * 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 * 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 loading without being on the library search path ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed learnErrors 6.434 0.720 3.820 PacBioErrfun 5.659 0.104 5.763 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘dada2-intro.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 10 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/dada2.Rcheck/00check.log’ for details.
dada2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL dada2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘dada2’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o In file included from ../inst/include/dada2.h:7, from RcppExports.cpp:4: ../inst/include/dada2_RcppExports.h:14:14: warning: ‘void dada2::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function] 14 | void validateSignature(const char* sig) { | ^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rmain.cpp -o Rmain.o Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’: Rmain.cpp:71:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 71 | if(quals.nrow() != maxlen) { | ~~~~~~~~~~~~~^~~~~~~~~ Rmain.cpp: In function ‘B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)’: Rmain.cpp:316:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 316 | while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) { | ~~~~~~~~~~~^~~~~~~~~~~ Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’: Rmain.cpp:290:9: warning: ‘kord’ may be used uninitialized in this function [-Wmaybe-uninitialized] 290 | free(kord); | ~~~~^~~~~~ Rmain.cpp:289:9: warning: ‘k16’ may be used uninitialized in this function [-Wmaybe-uninitialized] 289 | free(k16); | ~~~~^~~~~ Rmain.cpp:288:9: warning: ‘k8’ may be used uninitialized in this function [-Wmaybe-uninitialized] 288 | free(k8); | ~~~~^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c chimera.cpp -o chimera.o chimera.cpp: In function ‘bool C_is_bimera(std::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)’: chimera.cpp:25:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 25 | for(i=0;i<pars.size() && rval==false;i++) { | ~^~~~~~~~~~~~ chimera.cpp:29:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 29 | if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents" | ~~~~~~~~~~~~~^~~~~~~~~~~~ chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 44 | if((max_right+max_left)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp:48:83: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ chimera.cpp: In function ‘void get_lr(char**, int&, int&, int&, int&, bool, int)’: chimera.cpp:231:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 231 | while(al[0][pos] == '-' && pos<len) { | ~~~^~~~ chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 237 | while(pos<len && al[0][pos] == al[1][pos]) { | ~~~^~~~ chimera.cpp:244:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | if(pos<len && al[0][pos] != '-') { left_oo++; } | ~~~^~~~ chimera.cpp:245:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 245 | while(pos<len && al[0][pos] == al[1][pos]) { | ~~~^~~~ chimera.cpp:254:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 254 | while(al[1][pos] == '-' && pos>+(len-max_shift)) { | ~~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cluster.cpp -o cluster.o cluster.cpp: In function ‘void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’: cluster.cpp:17:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable] 17 | unsigned int index, cind, center_reads; | ^~~~ cluster.cpp: In function ‘void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’: cluster.cpp:166:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 166 | for(row=0;row<errMat.nrow();row++) { | ~~~^~~~~~~~~~~~~~ cluster.cpp:167:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 167 | for(col=0;col<errMat.ncol();col++) { | ~~~^~~~~~~~~~~~~~ cluster.cpp:156:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable] 156 | unsigned int index, cind, row, col, ncol; | ^~~~ cluster.cpp: In function ‘int b_bud(B*, double, int, int, bool)’: cluster.cpp:284:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 284 | for(i=0;i<b->nclust;i++) { | ~^~~~~~~~~~ cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 285 | for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center | ~^~~~~~~~~~~~~~~ cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 288 | if(raw->reads < min_abund) { continue; } | ~~~~~~~~~~~^~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c containers.cpp -o containers.o containers.cpp: In function ‘void b_free(B*)’: containers.cpp:141:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 141 | for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); } | ~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c error.cpp -o error.o error.cpp: In function ‘Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)’: error.cpp:178:51: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable] 178 | unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol; | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c evaluate.cpp -o evaluate.o evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::string, std::string)’: evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 88 | } while((s1gap || s2gap) && start<s1.size()); | ~~~~~^~~~~~~~~~ evaluate.cpp: In function ‘Rcpp::CharacterVector C_pair_consensus(std::string, std::string, int, bool)’: evaluate.cpp:133:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 133 | for(i=0;i<s1.size();i++) { | ~^~~~~~~~~~ evaluate.cpp:152:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 152 | for(i=0;i<s1.size();i++) { | ~^~~~~~~~~~ evaluate.cpp:163:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 163 | for(i=0;i<s1.size();i++) { | ~^~~~~~~~~~ evaluate.cpp: In function ‘Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’: evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 219 | for(int i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp: In function ‘Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)’: evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 243 | for(int i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for(int i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp: In function ‘Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’: evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 286 | for(int i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 298 | for(i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 310 | for(j=0;j<klen_min;j++) { | ~^~~~~~~~~ evaluate.cpp: In function ‘Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’: evaluate.cpp:339:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 339 | for(i=0;i<nseqs;i++) { | ~^~~~~~ evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 348 | for(j=0;j<n_kmers;j++) { | ~^~~~~~~~ evaluate.cpp:327:10: warning: variable ‘len1’ set but not used [-Wunused-but-set-variable] 327 | size_t len1 = 0, len2 = 0; | ^~~~ evaluate.cpp:327:20: warning: variable ‘len2’ set but not used [-Wunused-but-set-variable] 327 | size_t len1 = 0, len2 = 0; | ^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c filter.cpp -o filter.o filter.cpp: In function ‘Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::string, unsigned int, bool)’: filter.cpp:16:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 16 | for(i=0;i<len;i++) { | ~^~~~ filter.cpp:20:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 20 | for(i=0;i<seqs.size();i++) { | ~^~~~~~~~~~~~ filter.cpp:24:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 24 | for(j=0;j<=(len-word_size);j++) { | ~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c kmers.cpp -o kmers.o kmers.cpp: In function ‘double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)’: kmers.cpp:85:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for(i=0;i<STEP;i++) { | ~^~~~~ kmers.cpp: In function ‘double kord_dist(uint16_t*, int, uint16_t*, int, int)’: kmers.cpp:110:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 110 | for(i=0;i<klen;i++) { | ~^~~~~ kmers.cpp: In function ‘double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)’: kmers.cpp:141:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 141 | for(i=0;i<STEP;i++) { | ~^~~~~ kmers.cpp:144:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left | ~^~~~~ kmers.cpp: In function ‘void assign_kmer8(uint8_t*, const char*, int)’: kmers.cpp:162:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 162 | if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:174:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 174 | for(i=0; i<klen; i++) { | ~^~~~~ kmers.cpp: In function ‘void assign_kmer(uint16_t*, const char*, int)’: kmers.cpp:211:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 211 | if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:221:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 221 | for(i=0; i<klen; i++) { | ~^~~~~ kmers.cpp: In function ‘void assign_kmer_order(uint16_t*, char*, int)’: kmers.cpp:250:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 250 | if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); } | ~~^~~~~~ kmers.cpp:255:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for(i=0;i<klen;i++) { kord[i] = 0; } | ~^~~~~ kmers.cpp:257:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 257 | for(i=0; i<klen; i++) { | ~^~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 24 | for(int i=0;i<strlen(al0);i++) { | ~^~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 89 | for (i = 0; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (j = 0; j <= len2; j++) { | ~~^~~~~~~ nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:114:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:115:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for(i=0;i<=len1;i++) { | ~^~~~~~ nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 117 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; } | ~~~~~~~~~~^~~~~~~ nwalign_endsfree.cpp:122:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 122 | for (i = 1; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 125 | r = i+rband; if(r>len2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 130 | if (i == len1) { | ~~^~~~~~~ nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 137 | if (j == len2) { | ~~^~~~~~~ nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | for (i=0;i<len_al;i++) { | ~^~~~~~~ nwalign_endsfree.cpp: In function ‘char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)’: nwalign_endsfree.cpp:230:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | for (i=0,j=0;j<len1;j++) { | ~^~~~~ nwalign_endsfree.cpp:231:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 231 | if (j==len1-1 || s1[j]!=s1[j+1]) { | ~^~~~~~~~ nwalign_endsfree.cpp:244:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | for (i=0,j=0;j<len2;j++) { | ~^~~~~ nwalign_endsfree.cpp:245:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 245 | if (j==len2-1 || s2[j]!=s2[j+1]) { | ~^~~~~~~~ nwalign_endsfree.cpp:264:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 264 | for (i = 0; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 270 | for (j = 0; j <= len2; j++) { | ~~^~~~~~~ nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 289 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:289:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 289 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:290:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 290 | for(i=0;i<=len1;i++) { | ~^~~~~~ nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 292 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; } | ~~~~~~~~~~^~~~~~~ nwalign_endsfree.cpp:297:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 297 | for (i = 1; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 300 | r = i+rband; if(r>len2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 305 | if (i == len1) { | ~~^~~~~~~ nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 314 | if (j == len2) { | ~~^~~~~~~ nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 379 | for (i=0;i<len_al;i++) { | ~^~~~~~~ nwalign_endsfree.cpp: In function ‘char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)’: nwalign_endsfree.cpp:419:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 419 | for (i = 1; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 425 | for (j = 1; j <= len2; j++) { | ~~^~~~~~~ nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 444 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:444:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 444 | if(band>=0 && (band<len1 || band<len2)) { | ~~~~^~~~~ nwalign_endsfree.cpp:445:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 445 | for(i=0;i<=len1;i++) { | ~^~~~~~ nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 447 | if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; } | ~~~~~~~~~~^~~~~~~ nwalign_endsfree.cpp:452:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 452 | for (i = 1; i <= len1; i++) { | ~~^~~~~~~ nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 455 | r = i+rband; if(r>len2) { r = len2; } | ~^~~~~ nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 522 | for (i=0;i<len_al;i++) { | ~^~~~~~~ nwalign_endsfree.cpp: In function ‘char** nwalign_gapless(const char*, size_t, const char*, size_t)’: nwalign_endsfree.cpp:548:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 548 | for (int i=0;i<len_al;i++) { | ~^~~~~~~ nwalign_endsfree.cpp:549:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 549 | al[0][i] = i < len1 ? s1[i] : '-'; | ~~^~~~~~ nwalign_endsfree.cpp:550:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 550 | al[1][i] = i < len2 ? s2[i] : '-'; | ~~^~~~~~ nwalign_endsfree.cpp: In function ‘Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)’: nwalign_endsfree.cpp:658:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 658 | for(s=0;s<sub->nsubs;s++) { | ~^~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 96 | start_col = 1 + (1+(band<len1 ? band : len1))/2; | ~~~~^~~~~ nwalign_vectorized.cpp:125:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 125 | while(row < (1 + (band < len1 ? band : len1))) { | ~~~~~^~~~~~ nwalign_vectorized.cpp:178:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 178 | if(row==(band<len1 ? band : len1)) { | ~~~~^~~~~ nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 218 | 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] 75 | size_t start_col, end_col; | ^~~~~~~ nwalign_vectorized.cpp: In function ‘Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)’: nwalign_vectorized.cpp:330:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 330 | for(i=0;i<s1.size();i++) { | ~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c pval.cpp -o pval.o pval.cpp: In function ‘double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)’: pval.cpp:121:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 121 | for(s=0;s<sub->nsubs;s++) { | ~^~~~~~~~~~~ pval.cpp:123:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 123 | if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); } | ~~~~~^~~~~~~~~~~~ pval.cpp: In function ‘double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)’: pval.cpp:177:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 177 | for(s=0;s<sub->nsubs;s++) { | ~^~~~~~~~~~~ pval.cpp:179:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 179 | if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); } | ~~~~~^~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -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 unsigned int’} [-Wsign-compare] 48 | if(kmer>=0 && kmer<n_kmers) { | ~~~~^~~~~~~~ taxonomy.cpp: In function ‘int get_best_genus(int*, float*, unsigned int, unsigned int, unsigned int, float*)’: taxonomy.cpp:84:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 84 | for(g=0;g<ngenus;g++) { | ~^~~~~~~ taxonomy.cpp: In member function ‘virtual void AssignParallel::operator()(std::size_t, std::size_t)’: taxonomy.cpp:145:31: warning: variable ‘boot_match’ set but not used [-Wunused-but-set-variable] 145 | unsigned int boot, booti, boot_match, arraylen, arraylen_rc; | ^~~~~~~~~~ taxonomy.cpp: In function ‘Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)’: taxonomy.cpp:222:45: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 222 | if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) { taxonomy.cpp:252:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for(kmer=0;kmer<n_kmers;kmer++) { | ~~~~^~~~~~~~ taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 261 | for(kmer=0;kmer<n_kmers;kmer++) { | ~~~~^~~~~~~~ taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 268 | for(kmer=0;kmer<n_kmers;kmer++) { | ~~~~^~~~~~~~ taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 287 | for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); } | ~^~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o dada2.so 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 -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-dada2/00new/dada2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dada2)
dada2.Rcheck/dada2-Ex.timings
name | user | system | elapsed | |
PacBioErrfun | 5.659 | 0.104 | 5.763 | |
addSpecies | 3.156 | 0.220 | 3.376 | |
assignSpecies | 1.453 | 0.004 | 1.457 | |
assignTaxonomy | 0.209 | 0.008 | 0.212 | |
collapseNoMismatch | 0.574 | 0.004 | 0.579 | |
dada | 3.095 | 0.080 | 3.175 | |
derepFastq | 0.665 | 0.016 | 0.680 | |
fastqFilter | 0.428 | 0.000 | 0.429 | |
fastqPairedFilter | 1.363 | 0.072 | 1.436 | |
filterAndTrim | 0.762 | 0.016 | 0.778 | |
getDadaOpt | 0 | 0 | 0 | |
getErrors | 0.973 | 0.016 | 0.990 | |
getSequences | 0.301 | 0.004 | 0.305 | |
getUniques | 0.295 | 0.004 | 0.299 | |
inflateErr | 0.001 | 0.000 | 0.000 | |
isBimera | 0.070 | 0.000 | 0.069 | |
isBimeraDenovo | 2.422 | 0.012 | 2.433 | |
isBimeraDenovoTable | 2.262 | 0.008 | 2.270 | |
isPhiX | 0.181 | 0.008 | 0.188 | |
isShiftDenovo | 1.027 | 0.004 | 1.031 | |
learnErrors | 6.434 | 0.720 | 3.820 | |
loessErrfun | 0.323 | 0.000 | 0.324 | |
makeSequenceTable | 0.577 | 0.024 | 0.601 | |
mergePairs | 3.733 | 0.108 | 3.841 | |
mergeSequenceTables | 0.000 | 0.000 | 0.001 | |
noqualErrfun | 0.696 | 0.000 | 0.697 | |
nwalign | 0.000 | 0.000 | 0.001 | |
nwhamming | 0.000 | 0.000 | 0.001 | |
plotComplexity | 0.241 | 0.007 | 0.248 | |
plotErrors | 1.788 | 0.056 | 1.844 | |
plotQualityProfile | 3.475 | 0.259 | 3.685 | |
rc | 0.018 | 0.000 | 0.018 | |
removeBimeraDenovo | 2.389 | 0.165 | 2.554 | |
removePrimers | 0.186 | 0.000 | 0.187 | |
seqComplexity | 0.019 | 0.000 | 0.019 | |
setDadaOpt | 0.000 | 0.000 | 0.001 | |
uniquesToFasta | 0.066 | 0.000 | 0.066 | |