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build_failure.linux-64.yaml
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recipe_sha: 5c919f6b633856f69d99b0780dced89e8f97d57e82ae443694d07e3f4f432fe2 # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:17:52: error: 'const struct genomics::chromosome' has no member named 'length'
17 | if (off_target_abs_coords <= (int64_t)(chr.length-1)) {
| ^~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:21:40: error: 'const struct genomics::chromosome' has no member named 'length'
21 | off_target_abs_coords -= chr.length;
| ^~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:46:62: error: 'struct genomics::chromosome' has no member named 'length'
46 | if ((start_position < 0) || (end_position > (int64_t)c.length)) {
| ^~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:47:60: error: too many initializers for 'genomics::chromosome'
47 | return std::make_tuple(coordinates{chromosome{"", 0}, 0}, "");
| ^
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:46: error: 'uint64_t' was not declared in this scope
51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand);
| ^~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:5:1: note: 'uint64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
4 | #include "genomics/structures.hpp"
|#include <cstdint>
5 |
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:54: error: too many initializers for 'genomics::coordinates'
51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand);
| ^
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:41: error: expected primary-expression before '{' token
51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand);
| ^
make[2]: *** [bin/CMakeFiles/guidescan.dir/build.make:121: bin/CMakeFiles/guidescan.dir/genomics/structures.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/sequences.cxx: In function 'std::string genomics::complement(const std::string&)':
/opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/sequences.cxx:30:31: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
30 | for (int64_t i = 0; i < kmer.length(); i) {
| ~~^~~~~~~~~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx: In function 'int main(int, char**)':
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:335:8: warning: unused variable 'download' [-Wunused-variable]
335 | auto download = download_cmd(guidescan, download_opts);
| ^~~~~~~~
[ 91%] Linking CXX executable csa_sada_test
[ 91%] Built target csa_sada_test
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_lines(const genome_index<t_wt, t_dens, t_inv_dens>&, const kmer&, bool, int64_t, std::vector<std::vector<std::tuple<long int, match> > >&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; int64_t = long int]':
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const std::vector<kmer>&, std::ostream&, std::mutex&, std::atomic<long unsigned int>&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point<std::chrono::_V2::steady_clock, std::chrono::duration<long int, std::ratio<1, 1000000000> > >]'
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:257:29: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::vector<std::tuple<long int, genomics::match> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
257 | for (int64_t i = 0; i < off_targets[d].size(); i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:12:
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index<t_wt, t_dens, t_inv_dens>::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector<std::__cxx11::basic_string<char> >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function<void(genomics::match, t_data&)>&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; ssize_t = long int; size_t = long unsigned int]':
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index<t_wt, t_dens, t_inv_dens>::inexact_search(const std::string&, const std::vector<std::__cxx11::basic_string<char> >&, size_t, size_t, size_t, size_t, const std::function<void(genomics::match, t_data&)>&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; size_t = long unsigned int]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:67:32: required from 'void genomics::process_kmer_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const std::vector<kmer>&, std::ostream&, std::mutex&, std::atomic<long unsigned int>&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point<std::chrono::_V2::steady_clock, std::chrono::duration<long int, std::ratio<1, 1000000000> > >]'
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | && position != query.length() - 1) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
369 | && position != query.length() - 1 ) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index<t_wt, t_dens, t_inv_dens>::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector<std::__cxx11::basic_string<char> >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function<void(genomics::match, t_data&)>&, t_data&) const [with t_data = std::vector<std::set<genomics::match> >; t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; ssize_t = long int; size_t = long unsigned int]':
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index<t_wt, t_dens, t_inv_dens>::inexact_search(const std::string&, const std::vector<std::__cxx11::basic_string<char> >&, size_t, size_t, size_t, size_t, const std::function<void(genomics::match, t_data&)>&, t_data&) const [with t_data = std::vector<std::set<genomics::match> >; t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; size_t = long unsigned int]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:82:32: required from 'void genomics::process_kmer_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const std::vector<kmer>&, std::ostream&, std::mutex&, std::atomic<long unsigned int>&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point<std::chrono::_V2::steady_clock, std::chrono::duration<long int, std::ratio<1, 1000000000> > >]'
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
276 | && position != query.length() - 1) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
369 | && position != query.length() - 1 ) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_line_nomatch(const genome_index<t_wt, t_dens, t_inv_dens>&, const kmer&, bool, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>]':
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:288:39: required from 'std::string genomics::get_csv_lines(const genome_index<t_wt, t_dens, t_inv_dens>&, const kmer&, bool, int64_t, std::vector<std::vector<std::tuple<long int, match> > >&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string<char>; int64_t = long int]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>]'
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index<t_wt, t_dens, t_inv_dens>&, const genome_index<t_wt, t_dens, t_inv_dens>&, const enumerate_cmd_options&, const std::vector<kmer>&, std::ostream&, std::mutex&, std::atomic<long unsigned int>&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc<sdsl::huff_shape, sdsl::int_vector<1>, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream<char>; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point<std::chrono::_V2::steady_clock, std::chrono::duration<long int, std::ratio<1, 1000000000> > >]'
/opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here
/opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:190:84: warning: unused parameter 'gi' [-Wunused-parameter]
190 | std::string get_csv_line_nomatch(const genome_index<t_wt, t_dens, t_inv_dens>& gi,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
make[1]: *** [CMakeFiles/Makefile2:8238: bin/CMakeFiles/guidescan.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
Traceback (most recent call last):
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1734201456193/work/conda_build.sh']' returned non-zero exit status 2.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1734201456193/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.