[package - 131i386-default][biology/salmon] Failed for salmon-1.10.2 in build
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Date: Sat, 22 Jul 2023 20:11:30 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy15/data/131i386-default/150bed43bfd4/logs/salmon-1.10.2.log
Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=131i386-default&build=150bed43bfd4
Log:
=>> Building biology/salmon
build started at Sat Jul 22 20:10:16 UTC 2023
port directory: /usr/ports/biology/salmon
package name: salmon-1.10.2
building for: FreeBSD 131i386-default-job-03 13.1-RELEASE-p8 FreeBSD 13.1-RELEASE-p8 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
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Job Id: 03
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jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[131i386-default-job-03] Installing pkg-1.20.4...
[131i386-default-job-03] Extracting pkg-1.20.4: .......... done
===> salmon-1.10.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of salmon-1.10.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
=> COMBINE-lab-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz
fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/COMBINE-lab/salmon/tar.gz/v1.10.2?dummy=/COMBINE-lab-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known
COMBINE-lab-salmon-v1.10.2_GH0.tar.gz 7024 kB 10 MBps 01s
=> COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz
fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/COMBINE-lab/pufferfish/tar.gz/salmon-v1.10.2?dummy=/COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz: size of remote file is not known
COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz 3289 kB 5612 kBps 00s
=> jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz
fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-15?dummy=/jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz: size of remote file is not known
jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz 3302 kB 4708 kBps 01s
=> samtools-htscodecs-5aecc6e_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz
fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/samtools/htscodecs/tar.gz/5aecc6e?dummy=/samtools-htscodecs-5aecc6e_GH0.tar.gz: size of remote file is not known
samtools-htscodecs-5aecc6e_GH0.tar.gz 3116 kB 15 MBps 01s
===> Fetching all distfiles required by salmon-1.10.2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by salmon-1.10.2 for building
=> SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz.
=> SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz.
=> SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz.
=> SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
<snip>
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:37: error: non-constant-expression cannot be narrowed from type 'uint64_t' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing]
return PackedContigInfo{i, (*data_)[i], len};
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:37: note: insert an explicit cast to silence this issue
return PackedContigInfo{i, (*data_)[i], len};
^
static_cast<size_t>( )
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:40: error: non-constant-expression cannot be narrowed from type 'std::__vector_base<unsigned long long, std::allocator<unsigned long long>>::value_type' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing]
return PackedContigInfo{i, (*data_)[i], len};
^~~~~~~~~~~
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:1156:40: note: insert an explicit cast to silence this issue
return PackedContigInfo{i, (*data_)[i], len};
^~~~~~~~~~~
static_cast<size_t>( )
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:691:38: warning: format specifies type 'unsigned long' but the argument has type 'std::vector<unsigned long long>::size_type' (aka 'unsigned int') [-Wformat]
printf("rank array : size %lu \n",_ranks.size());
~~~ ^~~~~~~~~~~~~
%u
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:35: error: expected ')'
return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:21: note: to match this '('
return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:822:23: error: use of undeclared identifier '__uint128_t'
return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:819:46: warning: unused parameter 'word' [-Wunused-parameter]
static inline uint64_t fastrange64(uint64_t word, uint64_t p) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:819:61: warning: unused parameter 'p' [-Wunused-parameter]
static inline uint64_t fastrange64(uint64_t word, uint64_t p) {
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:27:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
mer_base_static(unsigned int k, const char* s) : super(k_) {
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long long, 2, unsigned long long, false, 64>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
lhs_setter& operator=(const lhs_setter& rhs) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:250:14: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long long, 2, unsigned long long, false, 64>' first required here
auto c = seqVec[i];
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:917:12: warning: variable 'totalKmersIshouldSee' set but not used [-Wunused-but-set-variable]
size_t totalKmersIshouldSee{0} ;
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, spp::sparsegroup<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>> *, std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, spp::sparsegroup<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>> *, std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>' first required here
for (destructive_iterator it = ht.destructive_begin();
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, unsigned long long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SelectKey, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SetKey, std::equal_to<unsigned long long>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>::_move_from' requested here
_move_from(mover, ht, min_buckets_wanted);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, unsigned long long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SelectKey, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SetKey, std::equal_to<unsigned long long>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>::sparse_hashtable' requested here
sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, unsigned long long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SelectKey, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SetKey, std::equal_to<unsigned long long>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>::_resize_delta' requested here
if (_resize_delta(1))
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>, unsigned long long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SelectKey, spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::SetKey, std::equal_to<unsigned long long>, spp::libc_allocator<std::pair<const unsigned long long, std::vector<std::pair<unsigned long long, bool>>>>>::find_or_insert<spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::DefaultValue, unsigned long long &>' requested here
return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned long long, std::vector<std::pair<unsigned long long, bool>>>::operator[]<unsigned long long &>' requested here
path[ref_cnt].resize(contigCntPerPath);
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long long, 8, unsigned long long, false, 64>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
lhs_setter& operator=(const lhs_setter& rhs) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long long, 8, unsigned long long, false, 64>' first required here
? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long long, 8>, unsigned long long, 8, unsigned long long, std::allocator<unsigned long long>, 64, false>::operator[]' requested here
for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0;
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long long, 0, unsigned long long, false, 64>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
lhs_setter& operator=(const lhs_setter& rhs) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long long, 0, unsigned long long, false, 64>' first required here
? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long long, unsigned long long, std::allocator<unsigned long long>, 64, false>, unsigned long long, 0, unsigned long long, std::allocator<unsigned long long>, 64, false>::operator[]' requested here
(*cpos_offsets)[0] = 0;
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>> *, std::pair<const std::vector<unsigned int>, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>> *, std::pair<const std::vector<unsigned int>, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>' first required here
for (destructive_iterator it = ht.destructive_begin();
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int>, unsigned int>, std::vector<unsigned int>, VecHasher, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SetKey, std::equal_to<std::vector<unsigned int>>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>::_move_from' requested here
_move_from(mover, ht, min_buckets_wanted);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int>, unsigned int>, std::vector<unsigned int>, VecHasher, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SetKey, std::equal_to<std::vector<unsigned int>>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>::sparse_hashtable' requested here
sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int>, unsigned int>, std::vector<unsigned int>, VecHasher, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SetKey, std::equal_to<std::vector<unsigned int>>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>::_resize_delta' requested here
if (_resize_delta(1))
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int>, unsigned int>, std::vector<unsigned int>, VecHasher, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::SetKey, std::equal_to<std::vector<unsigned int>>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int>>>::find_or_insert<spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::DefaultValue, std::vector<unsigned int> &>' requested here
return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, VecHasher>::operator[]<std::vector<unsigned int> &>' requested here
eqID = eqMap[tlist];
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long long, 1, unsigned long long, false, 64>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
lhs_setter& operator=(const lhs_setter& rhs) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long long, 1, unsigned long long, false, 64>' first required here
? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:120:20: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long long, 1>, unsigned long long, 1, unsigned long long, std::allocator<unsigned long long>, 64, false>::operator[]' requested here
return ((*rank_)[endPos] == 1);
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1032:8: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
totalsizeBitset, 100*(float)totalsizeBitset/totalsize);
^~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:660:46: note: in instantiation of member function 'boomphf::mphf<unsigned long long, boomphf::SingleHashFunctor<unsigned long long>>::totalBitSize' requested here
jointLog->info("mphf size = {} MB", (bphf->totalBitSize() / 8) / std::pow(2, 20));
^
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1034:8: warning: format specifies type 'unsigned long' but the argument has type 'unsigned int' [-Wformat]
_final_hash.size()*42*8, 100*(float)(_final_hash.size()*42*8)/totalsize,
^~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:1035:8: warning: format specifies type 'unsigned long' but the argument has type 'std::unordered_map<unsigned long long, unsigned long long, boomphf::SingleHashFunctor<unsigned long long>>::size_type' (aka 'unsigned int') [-Wformat]
_final_hash.size() );
^~~~~~~~~~~~~~~~~~
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24:
In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10:
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long long, 0, unsigned long long, true, 64>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]
lhs_setter& operator=(const lhs_setter& rhs) {
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long long, 0, unsigned long long, true, 64>' first required here
? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
^
/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:737:17: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long long, unsigned long long, std::allocator<unsigned long long>, 64, true>, unsigned long long, 0, unsigned long long, std::allocator<unsigned long long>, 64, true>::operator[]' requested here
posVec[idx] = kb1.pos();
^
23 warnings and 4 errors generated.
gmake[3]: *** [external/pufferfish/src/CMakeFiles/puffer.dir/build.make:79: external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:458: external/pufferfish/src/CMakeFiles/puffer.dir/all] Error 2
gmake[2]: *** Waiting for unfinished jobs....
[ 28%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o
cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -g -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
gmake[3]: *** [external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make:93: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o] Abort trap (core dumped)
gmake[3]: *** Waiting for unfinished jobs....
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:326: external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
gmake[1]: *** [Makefile:169: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/salmon