these 2 derivations will be built: /nix/store/fl3psvrw1rklfw5524x0gb6w14yzx6ss-source.drv /nix/store/5q2rkym12hbwczmy7wyc6wsqhbv8mzds-usalign-20260921.drv building '/nix/store/gycgzggsm3zaaaimmx70l60gw6z8wx79-source.drv' source> structuredAttrs is enabled source> source> trying https://github.com/pylelab/USalign/archive/1fa25a958fe3095900eba2ef9b48562bdc462251.tar.gz source> % Total % Received % Xferd Average Speed Time Time Time Current source> Dload Upload Total Spent Left Speed source> source> 0 0 0 0 0 0 0 0 0 source> 0 0 0 0 0 0 0 0 0 source> 0 0 0 0 0 0 0 0 0 source> source> 0 0 0 0 0 0 0 0 0 source> 100 278.7k 0 278.7k 0 0 358.5k 0 0 source> 100 278.7k 0 278.7k 0 0 358.4k 0 0 source> 100 278.7k 0 278.7k 0 0 358.4k 0 0 source> unpacking source archive /build/download.tar.gz building '/nix/store/5q2rkym12hbwczmy7wyc6wsqhbv8mzds-usalign-20260921.drv' usalign-20260921> Running phase: unpackPhase usalign-20260921> unpacking source archive /nix/store/1yakjjglvbrf5468ibsin05w9jr58a1k-source usalign-20260921> source root is source usalign-20260921> Running phase: patchPhase usalign-20260921> Running phase: updateAutotoolsGnuConfigScriptsPhase usalign-20260921> Running phase: configurePhase usalign-20260921> no configure script, doing nothing usalign-20260921> Running phase: buildPhase usalign-20260921> build flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash CC=c++ usalign-20260921> c++ -O3 -ffast-math qTMclust.cpp -o qTMclust usalign-20260921> c++ -O3 -ffast-math USalign.cpp -o USalign usalign-20260921> c++ -O3 -ffast-math USFlexalign.cpp -o USFlexalign usalign-20260921> c++ -O3 -ffast-math TMalign.cpp -o TMalign usalign-20260921> c++ -O3 -ffast-math TMscore.cpp -o TMscore usalign-20260921> c++ -O3 -ffast-math MMalign.cpp -o MMalign usalign-20260921> c++ -O3 -ffast-math se.cpp -o se usalign-20260921> c++ -O3 -ffast-math pdb2xyz.cpp -o pdb2xyz usalign-20260921> c++ -O3 -ffast-math xyz_sfetch.cpp -o xyz_sfetch usalign-20260921> c++ -O3 -ffast-math pdb2fasta.cpp -o pdb2fasta usalign-20260921> c++ -O3 -ffast-math biounitasym.cpp -o biounitasym usalign-20260921> c++ -O3 -ffast-math pdb2ss.cpp -o pdb2ss usalign-20260921> c++ -O3 -ffast-math NWalign.cpp -o NWalign usalign-20260921> c++ -O3 -ffast-math HwRMSD.cpp -o HwRMSD usalign-20260921> c++ -O3 -ffast-math cif2pdb.cpp -o cif2pdb usalign-20260921> c++ -O3 -ffast-math pdbAtomName.cpp -o pdbAtomName usalign-20260921> c++ -O3 -ffast-math addChainID.cpp -o addChainID usalign-20260921> In file included from addChainID.cpp:8: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from pdbAtomName.cpp:8: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from se.h:1, usalign-20260921> from se.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from TMscore.h:1, usalign-20260921> from TMscore.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from pdb2fasta.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from biounitasym.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from NWalign.h:5, usalign-20260921> from HwRMSD.h:3, usalign-20260921> from HwRMSD.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from cif2pdb.cpp:18: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from se.h:1, usalign-20260921> from MMalign.h:2, usalign-20260921> from MMalign.cpp:3: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from TMalign.cpp:3: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from se.h:1, usalign-20260921> from USFlexalign.cpp:3: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from se.h:1, usalign-20260921> from MMalign.h:2, usalign-20260921> from USalign.cpp:3: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from pdb2xyz.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from NWalign.h:5, usalign-20260921> from NWalign.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from param_set.h:7, usalign-20260921> from TMalign.h:6, usalign-20260921> from pdb2ss.cpp:1: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> In file included from basic_fun.h:23, usalign-20260921> from NWalign.h:5, usalign-20260921> from HwRMSD.h:3, usalign-20260921> from qTMclust.cpp:6: usalign-20260921> pstream.h: In member function 'bool redi::basic_pstreambuf::fill_buffer(bool)': usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h: In instantiation of 'bool redi::basic_pstreambuf::fill_buffer(bool) [with CharT = char; Traits = std::char_traits]': usalign-20260921> pstream.h:1867:17: required from 'std::streamsize redi::basic_pstreambuf::showmanyc() [with CharT = char; Traits = std::char_traits; std::streamsize = long int]' usalign-20260921> 1867 | avail = fill_buffer(true) ? this->egptr() - this->gptr() : -1; usalign-20260921> | ^~~~~~~~~~~ usalign-20260921> pstream.h:1863:5: required from here usalign-20260921> 1863 | basic_pstreambuf::showmanyc() usalign-20260921> | ^~~~~~~~~~~~~~~~~~~~~ usalign-20260921> pstream.h:1908:40: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1908 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> pstream.h:1920:38: warning: arithmetic between different enumeration types 'redi::pstreams::' and 'redi::pstreams::' is deprecated [-Wdeprecated-enum-enum-conversion] usalign-20260921> 1920 | rc = read(rbuf + pbsz, bufsz - pbsz); usalign-20260921> | ~~~~~~^~~~~~ usalign-20260921> buildPhase completed in 57 seconds usalign-20260921> Running phase: installPhase usalign-20260921> Running phase: fixupPhase usalign-20260921> shrinking RPATHs of ELF executables and libraries in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921 usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/qTMclust usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/USalign usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/TMalign usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/TMscore usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/MMalign usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/se usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2xyz usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/xyz_sfetch usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2fasta usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/biounitasym usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdb2ss usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/NWalign usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/HwRMSD usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/cif2pdb usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/pdbAtomName usalign-20260921> shrinking /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin/addChainID usalign-20260921> checking for references to /build/ in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921... usalign-20260921> patching script interpreter paths in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921 usalign-20260921> stripping (with command strip and flags -S -p) in /nix/store/lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921/bin post-build step Route build to niks3: ok Pushing SBEE-Lab/bioinformatics-toolkits to https://niks3.sjanglab.org time=2026-10-03T21:14:40.234+09:00 level=INFO msg="Uploading 1 paths to niks3.sjanglab.org (6 already cached)" time=2026-10-03T21:14:40.234+09:00 level=INFO msg="Uploading lb24jvkrz0mp3cp2c9vh8kwyf1ck5lky-usalign-20260921 (5.2MB)" time=2026-10-03T21:14:40.729+09:00 level=INFO msg="Uploading 1 narinfos" time=2026-10-03T21:14:41.079+09:00 level=INFO msg="Upload complete. 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