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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 ‘2.5.5’
** 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 v0.2.185
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 simd-adler32 v0.3.9
Compiling adler2 v2.0.1
Compiling once_cell v1.21.4
Compiling crc32fast v1.5.0
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 equivalent v1.0.2
Compiling typenum v1.20.0
Compiling either v1.15.0
Compiling getrandom v0.3.4
Compiling hashbrown v0.17.0
Compiling futures-core v0.3.32
Compiling futures-sink v0.3.32
Compiling lexical-util v1.0.7
Compiling paste v1.0.15
Compiling serde v1.0.228
Compiling futures-task v0.3.32
Compiling heck v0.5.0
Compiling futures-io v0.3.32
Compiling zstd-safe v7.2.4
Compiling slab v0.4.12
Compiling vcpkg v0.2.15
Compiling bytecount v0.6.9
Compiling bitflags v2.11.1
Compiling zstd-safe v6.0.6
Compiling rayon-core v1.13.0
Compiling semver v1.0.28
Compiling getrandom v0.4.2
Compiling rustversion v1.0.22
Compiling utf8parse v0.2.2
Compiling itoa v1.0.18
Compiling bytes v1.11.1
Compiling byteorder v1.5.0
Compiling snap v1.1.1
Compiling zmij v1.0.21
Compiling anyhow v1.0.102
Compiling unicode-width v0.2.2
Compiling lazy_static v1.5.0
Compiling rustix v1.1.4
Compiling fallible-streaming-iterator v0.1.9
Compiling linux-raw-sys v0.12.1
Compiling bit-vec v0.8.0
Compiling thiserror v1.0.69
Compiling is_terminal_polyfill v1.70.2
Compiling serde_json v1.0.149
Compiling anstyle-query v1.1.5
Compiling log v0.4.29
Compiling smallvec v1.15.1
Compiling colorchoice v1.0.5
Compiling anstyle v1.0.14
Compiling portable-atomic v1.13.1
Compiling static_assertions v1.1.0
Compiling array-init-cursor v0.2.1
Compiling clap_lex v1.1.0
Compiling fnv v1.0.7
Compiling twox-hash v1.6.3
Compiling thread_local v1.1.9
Compiling seq-macro v0.3.6
Compiling cpufeatures v0.2.17
Compiling fastrand v2.4.1
Compiling miniz_oxide v0.8.9
Compiling planus v0.3.1
Compiling sharded-slab v0.1.7
Compiling nu-ansi-term v0.50.3
Compiling tracing-core v0.1.36
Compiling itertools v0.13.0
Compiling strsim v0.11.1
Compiling itertools v0.14.0
Compiling streaming-iterator v0.1.9
Compiling base64 v0.22.1
Compiling hex v0.4.3
Compiling simdutf8 v0.1.5
Compiling number_prefix v0.4.0
Compiling ryu v1.0.23
Compiling anstyle-parse v1.0.0
Compiling generic-array v0.14.7
Compiling futures-channel v0.3.32
Compiling ahash v0.8.12
Compiling ethnum v1.5.3
Compiling foreign_vec v0.1.0
Compiling rustc_version v0.4.1
Compiling streaming-decompression v0.1.2
Compiling hash_hasher v2.0.4
Compiling arrayvec v0.7.6
Compiling base64 v0.21.7
Compiling dyn-clone v1.0.20
Compiling num-traits v0.2.19
Compiling matrixmultiply v0.3.10
Compiling num-complex v0.2.4
Compiling papergrid v0.14.0
Compiling path-tools v0.1.0
Compiling rustc-hash v2.1.2
Compiling parse-size v1.1.0
Compiling atomic_float v1.1.0
Compiling anstream v1.0.0
Compiling lz4_flex v0.10.0
Compiling aho-corasick v1.1.4
Compiling buffer-redux v1.1.0
Compiling csv-core v0.1.13
Compiling tracing-log v0.2.0
Compiling num-format v0.4.4
Compiling arrow2 v0.18.0
Compiling lexical-parse-integer v1.0.6
Compiling lexical-write-integer v1.0.6
Compiling indexmap v2.14.0
Compiling clap_builder v4.6.0
Compiling lexical-parse-float v1.0.6
Compiling crossbeam-epoch v0.9.18
Compiling crossbeam-channel v0.5.15
Compiling crossbeam-queue v0.3.12
Compiling lexical-write-float v1.0.6
Compiling crossbeam-deque v0.8.6
Compiling syn v2.0.117
Compiling proc-macro-error-attr2 v2.0.0
Compiling crossbeam v0.8.4
Compiling lexical-core v1.0.6
Compiling block-buffer v0.10.4
Compiling crypto-common v0.1.7
Compiling jobserver v0.1.34
Compiling digest v0.10.7
Compiling getrandom v0.2.17
Compiling num_cpus v1.17.0
Compiling console v0.15.11
Compiling cc v1.2.60
Compiling rayon v1.12.0
Compiling rand_core v0.6.4
Compiling rand_core v0.9.5
Compiling indicatif v0.17.11
Compiling regex-automata v0.4.14
Compiling tempfile v3.27.0
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 flate2 v1.1.9
Compiling num-bigint v0.4.6
Compiling num-iter v0.1.45
Compiling alga v0.9.3
Compiling noodles-bgzf v0.38.0
Compiling zstd-sys v2.0.16+zstd.1.5.7
Compiling bzip2-sys v0.1.13+1.0.8
Compiling liblzma-sys v0.3.13
Compiling libz-sys v1.1.28
Compiling sha2-asm v0.6.4
Compiling minimap2-sys v0.1.30+minimap2.2.30
Compiling lz4-sys v1.11.1+lz4-1.10.0
Compiling ndarray v0.16.1
Compiling ndarray v0.17.2
Compiling ndarray v0.15.6
Compiling csv v1.4.0
Compiling sha2 v0.10.9
Compiling num-rational v0.4.2
Compiling liblzma v0.3.6
Compiling num v0.4.3
Compiling proc-macro-error2 v2.0.1
Compiling ppv-lite86 v0.2.21
Compiling hashbrown v0.14.5
Compiling rand_chacha v0.3.1
Compiling rand_chacha v0.9.0
Compiling bytemuck_derive v1.10.2
Compiling futures-macro v0.3.32
Compiling serde_derive v1.0.228
Compiling async-trait v0.1.89
Compiling tracing-attributes v0.1.31
Compiling async-stream-impl v0.3.6
Compiling thiserror-impl v1.0.69
Compiling strum_macros v0.26.4
Compiling derive-new v0.6.0
Compiling clap_derive v4.6.1
Compiling typed-builder-macro v0.21.2
Compiling tabled_derive v0.10.0
Compiling rand v0.8.6
Compiling rand v0.9.4
Compiling async-stream v0.3.6
Compiling futures-util v0.3.32
Compiling bytemuck v1.25.0
Compiling tabled v0.18.0
Compiling tracing v0.1.44
Compiling safe_arch v0.7.4
Compiling rand_distr v0.4.3
Compiling typed-builder v0.21.2
Compiling bstr v1.12.1
Compiling matchers v0.2.0
Compiling regex v1.12.3
Compiling tracing-subscriber v0.3.23
Compiling wide v0.7.33
Compiling clap v4.6.1
Compiling bzip2 v0.4.4
Compiling noodles-core v0.17.0
Compiling noodles-csi v0.46.0
Compiling noodles-sam v0.74.0
Compiling simba v0.9.1
Compiling ndarray-stats v0.6.0
Compiling bincode v1.3.3
Compiling arrow-format v0.8.1
Compiling bio-types v1.0.4
Compiling kders v0.1.1
Compiling sendable-swapvec v0.4.3
Compiling noodles-bam v0.78.0
Compiling futures-executor v0.3.32
Compiling sprs v0.11.4
Compiling futures v0.3.32
Compiling parquet-format-safe v0.2.4
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 seqcol_rs v0.4.1
Compiling minimap2 v0.1.31+minimap2.2.30
Compiling statrs v0.18.0
Compiling oarfish v0.8.0
Finished `release` profile [optimized] target(s) in 48.30s
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)
