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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FLAMES
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** this is package ‘FLAMES’ version ‘2.6.0’
** using non-staged installation via StagedInstall field
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppFunctions.cpp -o RcppFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c classes/BamRecord.cpp -o classes/BamRecord.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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<StartEndPair>::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<int, int>::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<int, int>::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<std::__cxx11::basic_string<char>, Junctions>&, const std::unordered_map<std::__cxx11::basic_string<char>, Pos>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<StartEndPair> >&, GeneBlocks, std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >)’:
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<int>::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<int>::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-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
classes/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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::__cxx11::basic_string<char>, std::vector<StartEndPair> > get_gene_flat(const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<StartEndPair> >&)’:
classes/junctions.cpp:166:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<StartEndPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
166 | for (int i = 1; i < exons.size(); i++) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o
main-functions/flexiplex.cpp: In function ‘unsigned int edit_distance(const std::string&, const std::string&, unsigned int&, int)’:
main-functions/flexiplex.cpp:142:56: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
142 | if (j == (len2 - 1) && dist_holder[i * len2 + j] < best) {
main-functions/flexiplex.cpp: In function ‘void refine_matched_segments(const std::string&, const std::vector<Segment>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::unordered_set<std::__cxx11::basic_string<char> > >*, const std::vector<int>&, Barcode&, std::vector<int>&, std::vector<int>&)’:
main-functions/flexiplex.cpp:348:70: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
348 | } else if (editDistance < best_edit_distance && editDistance <= s.max_edit_distance) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp:356:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
356 | if (best_edit_distance <= s.max_edit_distance && current_segment_unambiguous) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
main-functions/flexiplex.cpp: In function ‘void print_read(const std::string&, const std::string&, const std::string&, const std::vector<Barcode>&, BGZF*, bool, bool, bool, const std::vector<Segment>&, const std::unordered_map<std::__cxx11::basic_string<char>, BarcodeGroup>&)’:
main-functions/flexiplex.cpp:790:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
790 | for (int b = 0; b < vec_size; b++) {
| ~~^~~~~~~~~~
main-functions/flexiplex.cpp:803:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
803 | for (int k = 0; k < vec_size; k++) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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 std::string&, const std::string&, const std::string&, int)’:
main-functions/get_transcript_seq.cpp:87:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
88 | if (i + wrap_len > seq.size()) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -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<char>, std::__cxx11::basic_string<char> > parseSpace(const std::string&)’:
main-functions/../utility/utility.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::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-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o
main-functions/pileup_readid.cpp: In function ‘Rcpp::NumericMatrix variant_count_matrix_cpp(Rcpp::String, Rcpp::String, int, bool, bool)’:
main-functions/pileup_readid.cpp:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
268 | for (int i = 0; i < BASES.size(); i++) {
| ~~^~~~~~~~~~~~~~
main-functions/pileup_readid.cpp: In instantiation of ‘std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::vector<std::__cxx11::basic_string<char> > > > group_umis(const TableType&, int) [with TableType = std::unordered_map<std::__cxx11::basic_string<char>, std::unordered_map<std::__cxx11::basic_string<char>, std::unordered_map<std::__cxx11::basic_string<char>, unsigned int> > >]’:
main-functions/pileup_readid.cpp:342:30: required from here
main-functions/pileup_readid.cpp:86:16: warning: unused variable ‘end’ [-Wunused-variable]
86 | unsigned int end;
| ^~~
main-functions/pileup_readid.cpp: In instantiation of ‘std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::vector<std::__cxx11::basic_string<char> > > > group_umis(const TableType&, int) [with TableType = std::unordered_map<std::__cxx11::basic_string<char>, std::unordered_map<std::__cxx11::basic_string<char>, std::array<unsigned int, 5> > >]’:
main-functions/pileup_readid.cpp:344:30: required from here
main-functions/pileup_readid.cpp:86:16: warning: unused variable ‘end’ [-Wunused-variable]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tests/test-junctions.cpp -o tests/test-junctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tests/test-parsing.cpp -o tests/test-parsing.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utility/cigars.cpp -o utility/cigars.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utility/bam.c -o utility/bam.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-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/edlib-1.2.7/edlib.o utility/bam.o -pthread -lz /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.23-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
Building for x86_64
(cd submodule/minimap2 && make -f Makefile CFLAGS="-g -O2 -Wall -Werror=format-security -Wno-unused-result" minimap2)
make[1]: Entering directory '/home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/submodule/minimap2'
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC main.c -o main.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC kthread.c -o kthread.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC kalloc.c -o kalloc.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC misc.c -o misc.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC bseq.c -o bseq.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC sketch.c -o sketch.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC sdust.c -o sdust.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC options.c -o options.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC index.c -o index.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC lchain.c -o lchain.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC align.c -o align.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC hit.c -o hit.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC seed.c -o seed.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC jump.c -o jump.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC map.c -o map.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC format.c -o format.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC pe.c -o pe.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC esterr.c -o esterr.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -DHAVE_KALLOC splitidx.c -o splitidx.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
cc -c -g -O2 -Wall -Werror=format-security -Wno-unused-result -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o jump.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
ar: `u' modifier ignored since `D' is the default (see `U')
cc -g -O2 -Wall -Werror=format-security -Wno-unused-result main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
make[1]: Leaving directory '/home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/submodule/minimap2'
echo "Installing binary to /home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/../inst/bin"
Installing binary to /home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/../inst/bin
mkdir -p ../inst/bin
cp submodule/minimap2/minimap2 ../inst/bin/
Building oarfish with cargo
mkdir -p ../inst/bin
mkdir cargo_temp
(cargo install oarfish --root cargo_temp --bin oarfish --vers 0.8.0)
Updating crates.io index
Installing oarfish v0.8.0
Updating crates.io index
Locking 279 packages to latest compatible versions
Adding generic-array v0.14.7 (available: v0.14.9)
Adding indicatif v0.17.11 (available: v0.18.4)
Adding needletail v0.6.3 (available: v0.7.3)
Adding noodles-bam v0.78.0 (available: v0.88.0)
Adding noodles-bgzf v0.38.0 (available: v0.46.0)
Adding noodles-sam v0.74.0 (available: v0.84.0)
Adding rand v0.9.4 (available: v0.10.1)
Adding tabled v0.18.0 (available: v0.20.0)
Adding typed-builder v0.21.2 (available: v0.23.2)
Compiling libc v0.2.186
Compiling proc-macro2 v1.0.106
Compiling quote v1.0.45
Compiling unicode-ident v1.0.24
Compiling shlex v1.3.0
Compiling find-msvc-tools v0.1.9
Compiling cfg-if v1.0.4
Compiling autocfg v1.5.0
Compiling pkg-config v0.3.33
Compiling libm v0.2.16
Compiling memchr v2.8.0
Compiling zerocopy v0.8.48
Compiling crossbeam-utils v0.8.21
Compiling version_check v0.9.5
Compiling crc32fast v1.5.0
Compiling adler2 v2.0.1
Compiling simd-adler32 v0.3.9
Compiling once_cell v1.21.4
Compiling regex-syntax v0.8.10
Compiling serde_core v1.0.228
Compiling zlib-rs v0.6.3
Compiling pin-project-lite v0.2.17
Compiling rawpointer v0.2.1
Compiling hashbrown v0.17.0
Compiling equivalent v1.0.2
Compiling typenum v1.20.0
Compiling getrandom v0.3.4
Compiling futures-core v0.3.32
Compiling either v1.15.0
Compiling lexical-util v1.0.7
Compiling paste v1.0.15
Compiling serde v1.0.228
Compiling futures-sink v0.3.32
Compiling futures-task v0.3.32
Compiling zstd-safe v7.2.4
Compiling vcpkg v0.2.15
Compiling futures-io v0.3.32
Compiling slab v0.4.12
Compiling heck v0.5.0
Compiling bytecount v0.6.9
Compiling bitflags v2.11.1
Compiling zstd-safe v6.0.6
Compiling bytes v1.11.1
Compiling utf8parse v0.2.2
Compiling rayon-core v1.13.0
Compiling semver v1.0.28
Compiling rustix v1.1.4
Compiling lazy_static v1.5.0
Compiling getrandom v0.4.2
Compiling itoa v1.0.18
Compiling anyhow v1.0.102
Compiling byteorder v1.5.0
Compiling zmij v1.0.21
Compiling unicode-width v0.2.2
Compiling snap v1.1.1
Compiling rustversion v1.0.22
Compiling array-init-cursor v0.2.1
Compiling fallible-streaming-iterator v0.1.9
Compiling serde_json v1.0.149
Compiling log v0.4.29
Compiling anstyle-query v1.1.5
Compiling smallvec v1.15.1
Compiling thiserror v1.0.69
Compiling bit-vec v0.8.0
Compiling static_assertions v1.1.0
Compiling is_terminal_polyfill v1.70.2
Compiling colorchoice v1.0.5
Compiling anstyle v1.0.14
Compiling portable-atomic v1.13.1
Compiling linux-raw-sys v0.12.1
Compiling strsim v0.11.1
Compiling fnv v1.0.7
Compiling sharded-slab v0.1.7
Compiling thread_local v1.1.9
Compiling clap_lex v1.1.0
Compiling fastrand v2.4.1
Compiling cpufeatures v0.2.17
Compiling nu-ansi-term v0.50.3
Compiling seq-macro v0.3.6
Compiling miniz_oxide v0.8.9
Compiling tracing-core v0.1.36
Compiling twox-hash v1.6.3
Compiling ethnum v1.5.3
Compiling futures-channel v0.3.32
Compiling rustc_version v0.4.1
Compiling ryu v1.0.23
Compiling planus v0.3.1
Compiling foreign_vec v0.1.0
Compiling simdutf8 v0.1.5
Compiling number_prefix v0.4.0
Compiling base64 v0.21.7
Compiling anstyle-parse v1.0.0
Compiling streaming-iterator v0.1.9
Compiling arrayvec v0.7.6
Compiling generic-array v0.14.7
Compiling ahash v0.8.12
Compiling dyn-clone v1.0.20
Compiling hash_hasher v2.0.4
Compiling base64 v0.22.1
Compiling hex v0.4.3
Compiling rustc-hash v2.1.2
Compiling atomic_float v1.1.0
Compiling path-tools v0.1.0
Compiling parse-size v1.1.0
Compiling num-traits v0.2.19
Compiling matrixmultiply v0.3.10
Compiling num-complex v0.2.4
Compiling itertools v0.13.0
Compiling papergrid v0.14.0
Compiling itertools v0.14.0
Compiling aho-corasick v1.1.4
Compiling buffer-redux v1.1.0
Compiling streaming-decompression v0.1.2
Compiling csv-core v0.1.13
Compiling lexical-write-integer v1.0.6
Compiling lexical-parse-integer v1.0.6
Compiling anstream v1.0.0
Compiling lz4_flex v0.10.0
Compiling num-format v0.4.4
Compiling tracing-log v0.2.0
Compiling arrow2 v0.18.0
Compiling lexical-parse-float v1.0.6
Compiling clap_builder v4.6.0
Compiling lexical-write-float v1.0.6
Compiling indexmap v2.14.0
Compiling syn v2.0.117
Compiling crossbeam-epoch v0.9.18
Compiling crossbeam-channel v0.5.15
Compiling crossbeam-queue v0.3.12
Compiling proc-macro-error-attr2 v2.0.0
Compiling lexical-core v1.0.6
Compiling block-buffer v0.10.4
Compiling crypto-common v0.1.7
Compiling crossbeam-deque v0.8.6
Compiling digest v0.10.7
Compiling getrandom v0.2.17
Compiling console v0.15.11
Compiling num_cpus v1.17.0
Compiling crossbeam v0.8.4
Compiling jobserver v0.1.34
Compiling rand_core v0.6.4
Compiling rand_core v0.9.5
Compiling cc v1.2.61
Compiling indicatif v0.17.11
Compiling rayon v1.12.0
Compiling tempfile v3.27.0
Compiling flate2 v1.1.9
Compiling regex-automata v0.4.14
Compiling num-integer v0.1.46
Compiling num-complex v0.4.6
Compiling approx v0.5.1
Compiling approx v0.3.2
Compiling noisy_float v0.2.1
Compiling chrono v0.4.44
Compiling noodles-bgzf v0.38.0
Compiling num-bigint v0.4.6
Compiling num-iter v0.1.45
Compiling alga v0.9.3
Compiling zstd-sys v2.0.16+zstd.1.5.7
Compiling liblzma-sys v0.3.13
Compiling bzip2-sys v0.1.13+1.0.8
Compiling libz-sys v1.1.28
Compiling sha2-asm v0.6.4
Compiling lz4-sys v1.11.1+lz4-1.10.0
Compiling minimap2-sys v0.1.30+minimap2.2.30
Compiling ndarray v0.16.1
Compiling ndarray v0.17.2
Compiling ndarray v0.15.6
Compiling sha2 v0.10.9
Compiling csv v1.4.0
Compiling proc-macro-error2 v2.0.1
Compiling num-rational v0.4.2
Compiling liblzma v0.3.6
Compiling bytemuck_derive v1.10.2
Compiling serde_derive v1.0.228
Compiling futures-macro v0.3.32
Compiling async-trait v0.1.89
Compiling async-stream-impl v0.3.6
Compiling tracing-attributes v0.1.31
Compiling thiserror-impl v1.0.69
Compiling typed-builder-macro v0.21.2
Compiling derive-new v0.6.0
Compiling tabled_derive v0.10.0
Compiling strum_macros v0.26.4
Compiling clap_derive v4.6.1
Compiling num v0.4.3
Compiling async-stream v0.3.6
Compiling ppv-lite86 v0.2.21
Compiling hashbrown v0.14.5
Compiling futures-util v0.3.32
Compiling rand_chacha v0.3.1
Compiling rand_chacha v0.9.0
Compiling tabled v0.18.0
Compiling rand v0.9.4
Compiling rand v0.8.6
Compiling tracing v0.1.44
Compiling bytemuck v1.25.0
Compiling typed-builder v0.21.2
Compiling safe_arch v0.7.4
Compiling wide v0.7.33
Compiling bzip2 v0.4.4
Compiling clap v4.6.1
Compiling rand_distr v0.4.3
Compiling bstr v1.12.1
Compiling matchers v0.2.0
Compiling regex v1.12.3
Compiling tracing-subscriber v0.3.23
Compiling noodles-core v0.17.0
Compiling noodles-csi v0.46.0
Compiling arrow-format v0.8.1
Compiling bincode v1.3.3
Compiling bio-types v1.0.4
Compiling ndarray-stats v0.6.0
Compiling noodles-sam v0.74.0
Compiling simba v0.9.1
Compiling sendable-swapvec v0.4.3
Compiling kders v0.1.1
Compiling futures-executor v0.3.32
Compiling futures v0.3.32
Compiling parquet-format-safe v0.2.4
Compiling sprs v0.11.4
Compiling noodles-bam v0.78.0
Compiling lz4 v1.28.1
Compiling nalgebra v0.33.3
Compiling zstd v0.12.4
Compiling zstd v0.13.3
Compiling parquet2 v0.17.2
Compiling needletail v0.6.3
Compiling minimap2 v0.1.31+minimap2.2.30
Compiling seqcol_rs v0.4.1
Compiling statrs v0.18.0
Compiling oarfish v0.8.0
Finished `release` profile [optimized] target(s) in 49.13s
Installing /home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/cargo_temp/bin/oarfish
Installed package `oarfish v0.8.0` (executable `oarfish`)
warning: be sure to add `/home/biocbuild/bbs-3.23-bioc/meat/FLAMES/src/cargo_temp/bin` to your PATH to be able to run the installed binaries
cp cargo_temp/bin/oarfish ../inst/bin/
cargo uninstall oarfish --root cargo_temp
Removing cargo_temp/bin/oarfish
rm -rf cargo_temp
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/FLAMES/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FLAMES)
