############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FLAMES ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘FLAMES’ ... ** using non-staged installation via StagedInstall field ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppFunctions.cpp -o RcppFunctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c classes/BamRecord.cpp -o classes/BamRecord.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c classes/GFFRecord.cpp -o classes/GFFRecord.o In file included from classes/GFFRecord.cpp:8: classes/../utility/utility.h: In function ‘std::pair, std::__cxx11::basic_string > parseSpace(const string&)’: classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for (int i = 0; i < s.size(); i++) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c classes/GeneAnnotationParser.cpp -o classes/GeneAnnotationParser.o In file included from classes/GeneAnnotationParser.cpp:15: classes/../utility/utility.h: In function ‘std::pair, std::__cxx11::basic_string > parseSpace(const string&)’: classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for (int i = 0; i < s.size(); i++) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c classes/Isoforms.cpp -o classes/Isoforms.o In file included from classes/Isoforms.cpp:16: classes/../utility/utility.h: In function ‘std::pair, std::__cxx11::basic_string > parseSpace(const string&)’: classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for (int i = 0; i < s.size(); i++) { | ~~^~~~~~~~~~ classes/Isoforms.cpp: In member function ‘void Isoforms::update_all_splice()’: classes/Isoforms.cpp:233:35: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 233 | if (blocks.size() >= (int)this->Min_sup_cnt) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ classes/Isoforms.cpp: In member function ‘void Isoforms::filter_TSS_TES(std::ofstream&, DoubleJunctions, float)’: classes/Isoforms.cpp:368:33: warning: comparison of integer expressions of different signedness: ‘std::unordered_map::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 368 | if ((left_counts.size() < (int)this->Min_sup_cnt) || | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ classes/Isoforms.cpp:369:38: warning: comparison of integer expressions of different signedness: ‘std::unordered_map::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 369 | (right_counts.size() < (int)this->Min_sup_cnt)) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ classes/Isoforms.cpp: In member function ‘void Isoforms::match_known_annotation(const std::unordered_map, Junctions>&, const std::unordered_map, Pos>&, const std::unordered_map, std::vector >&, GeneBlocks, std::unordered_map, std::__cxx11::basic_string >)’: classes/Isoforms.cpp:662:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 662 | for (int j = 0; j < std::min(raw_iso_key.size() - 1, junction.junctions.size()); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ classes/Isoforms.cpp:713:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 713 | for (int i = 0; i < new_exons.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~ classes/Isoforms.cpp:725:46: warning: comparisons like ‘X<=Y<=Z’ do not have their mathematical meaning [-Wparentheses] 725 | } else if (0 < i < raw_iso_key.size() - 1) { // a site from the middle somewhere | ~~^~~ classes/Isoforms.cpp: In member function ‘std::string Isoforms::isoform_to_gff3(float)’: classes/Isoforms.cpp:1140:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1140 | for (int i = 0; i < exons.size(); i+=2) { | ~~^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c classes/junctions.cpp -o classes/junctions.o In file included from classes/junctions.cpp:12: classes/../utility/utility.h: In function ‘std::pair, std::__cxx11::basic_string > parseSpace(const string&)’: classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for (int i = 0; i < s.size(); i++) { | ~~^~~~~~~~~~ classes/junctions.cpp: In function ‘std::unordered_map, std::vector > get_gene_flat(const std::unordered_map, std::vector > >&, const std::unordered_map, std::vector >&)’: classes/junctions.cpp:162:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 162 | for (int i = 1; i < exons.size(); i++) { | ~~^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o main-functions/flexiplex.cpp: In function ‘unsigned int edit_distance(const string&, const string&, unsigned int&, int)’: main-functions/flexiplex.cpp:119:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 119 | if (min_value <= max_editd) | ~~~~~~~~~~^~~~~~~~~~~~ main-functions/flexiplex.cpp: In function ‘Barcode get_barcode(const string&, const std::unordered_set >&, int, int, const std::vector, std::__cxx11::basic_string > >&)’: main-functions/flexiplex.cpp:225:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 225 | if (i_pattern >= subpattern_ends[i_subpattern]) { main-functions/flexiplex.cpp:286:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 286 | if (editDistance == barcode.editd) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:288:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 288 | } else if (editDistance < barcode.editd && | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:289:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 289 | editDistance <= barcode_max_editd) { // if best so far, update | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp: In function ‘std::vector big_barcode_search(const string&, const std::unordered_set >&, int, int, const std::vector, std::__cxx11::basic_string > >&)’: main-functions/flexiplex.cpp:351:29: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 351 | if (barcode.flank_end == std::string::npos) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp: In function ‘void print_stats(const string&, const std::vector&, std::ostream&)’: main-functions/flexiplex.cpp:376:38: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 376 | << (barcode.flank_end == std::string::npos ? "True" : "False") | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp: In function ‘void print_read(const string&, const string&, const string&, const std::vector&, std::ofstream&, std::unordered_set >&, bool)’: main-functions/flexiplex.cpp:401:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 401 | for (int b = 0; b < vec_bc.size(); b++) { | ~~^~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:411:32: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 411 | if (vec_bc.at(b).flank_end == std::string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:416:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 416 | for (int f = 0; f < vec_bc.size(); f++) { | ~~^~~~~~~~~~~~~~~ main-functions/flexiplex.cpp: In function ‘int flexiplex_cpp(Rcpp::String, Rcpp::String, bool, int, int, Rcpp::StringVector, Rcpp::String, Rcpp::String, Rcpp::String, int)’: main-functions/flexiplex.cpp:635:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 635 | for (int t = 0; t < sr_v.size(); | ~~^~~~~~~~~~~~~ main-functions/flexiplex.cpp:640:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 640 | for (int r = 0; r < sr_v[t].size(); r++) { // loop over the reads | ~~^~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:642:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 642 | for (int b = 0; b < sr_v[t][r].vec_bc_for.size(); b++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main-functions/flexiplex.cpp:644:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 644 | for (int b = 0; b < sr_v[t][r].vec_bc_rev.size(); b++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/get_transcript_seq.cpp -o main-functions/get_transcript_seq.o main-functions/get_transcript_seq.cpp: In function ‘void write_fa(const string&, const string&, const string&, int)’: main-functions/get_transcript_seq.cpp:87:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 87 | while (i < seq.size()) { | ~~^~~~~~~~~~~~ main-functions/get_transcript_seq.cpp:88:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 88 | if (i + wrap_len > seq.size()) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/group_bam2isoform.cpp -o main-functions/group_bam2isoform.o In file included from main-functions/group_bam2isoform.cpp:18: main-functions/../utility/utility.h: In function ‘std::pair, std::__cxx11::basic_string > parseSpace(const string&)’: main-functions/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | for (int i = 0; i < s.size(); i++) { | ~~^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c tests/test-junctions.cpp -o tests/test-junctions.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c tests/test-parsing.cpp -o tests/test-parsing.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/cigars.cpp -o utility/cigars.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/bam.c -o utility/bam.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw.c -o utility/ssw/ssw.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o classes/BamRecord.o classes/GFFRecord.o classes/GeneAnnotationParser.o classes/Isoforms.o classes/junctions.o main-functions/find_isoform.o main-functions/flexiplex.o main-functions/get_transcript_seq.o main-functions/group_bam2isoform.o main-functions/pileup_readid.o tests/test-junctions.o tests/test-parsing.o utility/cigars.o utility/edit_dist.o utility/fastq_utils.o utility/edlib-1.2.7/edlib.o utility/ssw/ssw_cpp.o utility/bam.o utility/ssw/ssw.o -pthread /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug FLAMES.so; fi installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/FLAMES/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 * DONE (FLAMES)