Running phase: unpackPhase unpacking source archive /nix/store/1yakjjglvbrf5468ibsin05w9jr58a1k-source source root is source Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase no configure script, doing nothing Running phase: buildPhase build flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash CC=c++ c++ -O3 -ffast-math qTMclust.cpp -o qTMclust c++ -O3 -ffast-math USalign.cpp -o USalign c++ -O3 -ffast-math USFlexalign.cpp -o USFlexalign c++ -O3 -ffast-math TMalign.cpp -o TMalign c++ -O3 -ffast-math TMscore.cpp -o TMscore c++ -O3 -ffast-math MMalign.cpp -o MMalign c++ -O3 -ffast-math se.cpp -o se c++ -O3 -ffast-math pdb2xyz.cpp -o pdb2xyz c++ -O3 -ffast-math xyz_sfetch.cpp -o xyz_sfetch c++ -O3 -ffast-math pdb2fasta.cpp -o pdb2fasta c++ -O3 -ffast-math biounitasym.cpp -o biounitasym c++ -O3 -ffast-math pdb2ss.cpp -o pdb2ss c++ -O3 -ffast-math NWalign.cpp -o NWalign c++ -O3 -ffast-math HwRMSD.cpp -o HwRMSD c++ -O3 -ffast-math cif2pdb.cpp -o cif2pdb c++ -O3 -ffast-math pdbAtomName.cpp -o pdbAtomName c++ -O3 -ffast-math addChainID.cpp -o addChainID In file included from addChainID.cpp:8: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from pdbAtomName.cpp:8: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from se.h:1, from se.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from TMscore.h:1, from TMscore.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from pdb2fasta.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from biounitasym.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from NWalign.h:5, from HwRMSD.h:3, from HwRMSD.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from cif2pdb.cpp:18: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from se.h:1, from MMalign.h:2, from MMalign.cpp:3: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from TMalign.cpp:3: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from se.h:1, from USFlexalign.cpp:3: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from se.h:1, from MMalign.h:2, from USalign.cpp:3: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from pdb2xyz.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from NWalign.h:5, from NWalign.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from param_set.h:7, from TMalign.h:6, from pdb2ss.cpp:1: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ In file included from basic_fun.h:23, from NWalign.h:5, from HwRMSD.h:3, from qTMclust.cpp:6: pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; | ^~~~~~~~~~~ pstream.h:1863:5: required from here 1863 | basic_pstreambuf::showmanyc() | ^~~~~~~~~~~~~~~~~~~~~ pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); | ~~~~~~^~~~~~ buildPhase completed in 57 seconds Running phase: installPhase Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921 shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/qTMclust shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/USalign shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/TMalign shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/TMscore shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/MMalign shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/se shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2xyz shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/xyz_sfetch shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2fasta shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/biounitasym shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2ss shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/NWalign shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/HwRMSD shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/cif2pdb shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdbAtomName shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/addChainID checking for references to /build/ in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921... patching script interpreter paths in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921 stripping (with command strip and flags -S -p) in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin