* Package:    sci-chemistry/modeller-9.25:0
 * Repository: gentoo
 * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_10
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/b5413ad911df4f773b098d897b5e27c05a80936b  (Mon Jan 29 12:03:14 UTC 2024)
@@@@@ END @@@@@



##################
# emerge --info: #
##################
Portage 3.0.61 (python 3.12.1-final-0, default/linux/amd64/17.1, gcc-14, glibc-2.38-r9, 6.1.66-gentoo-dist x86_64)
=================================================================
System uname: Linux-6.1.66-gentoo-dist-x86_64-AMD_EPYC_7513_32-Core_Processor-with-glibc2.38
KiB Mem:   263452516 total,  51858048 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Mon, 29 Jan 2024 12:03:14 +0000
sh bash 5.2_p26
ld GNU ld (Gentoo 2.41 p5) 2.41.0
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.2_p26::gentoo
dev-build/autoconf:        2.72-r1::gentoo
dev-build/automake:        1.16.5-r1::gentoo
dev-build/cmake:           3.28.1-r1::gentoo
dev-build/libtool:         2.4.7-r2::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.3.1-r1::gentoo
dev-lang/perl:             5.38.2-r1::gentoo
dev-lang/python:           3.10.13::gentoo, 3.11.7::gentoo, 3.12.1_p1::gentoo
sys-apps/baselayout:       2.14-r1::gentoo
sys-apps/openrc:           0.53::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-devel/binutils:        2.41-r5::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/gcc:             14.0.0_pre20231217::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-kernel/linux-headers:  6.7::gentoo (virtual/os-headers)
sys-libs/glibc:            2.38-r9::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    volatile: True
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 3
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* modeller"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
DISTDIR="/var/tmp/portage/sci-chemistry/modeller-9.25/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b --backtrack=100"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME"
FCFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
LEX="flex"
MAKEOPTS="-j32"
PKGDIR="/root/tbci/binpkg"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
SHELL="/bin/bash"
USE="acl amd64 bzip2 cli crypt debug dri elogind fortran gdbm iconv ipv6 jumbo-build libtirpc multilib native-symlinks ncurses nls openmp pam pcre readline seccomp split-usr ssl test-rust unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_10"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS





##############################
# emerge history (qlop -mv): #
##############################
2024-01-29T13:22:45 >>> dev-lang/swig-4.2.0




#######################################
# installed packages (qlist -ICvUSS): #
#######################################
acct-group/audio-0-r2:0
acct-group/cdrom-0-r2:0
acct-group/dialout-0-r2:0
acct-group/disk-0-r2:0
acct-group/floppy-0-r1:0
acct-group/input-0-r2:0
acct-group/kmem-0-r2:0
acct-group/kvm-0-r2:0
acct-group/lp-0-r2:0
acct-group/man-0-r2:0
acct-group/messagebus-0-r2:0
acct-group/polkitd-0-r2:0
acct-group/portage-0-r1:0
acct-group/render-0-r2:0
acct-group/root-0-r1:0
acct-group/sgx-0-r1:0
acct-group/sshd-0-r2:0
acct-group/tape-0-r2:0
acct-group/tty-0-r2:0
acct-group/usb-0-r2:0
acct-group/video-0-r2:0
acct-user/man-1-r2:0
acct-user/messagebus-0-r2:0
acct-user/polkitd-0-r2:0
acct-user/portage-0-r2:0
acct-user/sshd-0-r2:0
app-admin/eselect-1.4.27-r1:0 -doc -emacs -vim-syntax
app-admin/perl-cleaner-2.31:0 -pkgcore
app-alternatives/awk-4:0 -busybox gawk -mawk -nawk split-usr
app-alternatives/bc-0:0 -gh gnu
app-alternatives/bzip2-1:0 -lbzip2 -pbzip2 reference split-usr
app-alternatives/cpio-0:0 gnu -libarchive split-usr
app-alternatives/gzip-1:0 -pigz reference split-usr
app-alternatives/lex-0-r1:0 flex -reflex
app-alternatives/ninja-1:0 reference -samurai
app-alternatives/sh-0:0 bash -busybox -dash -ksh -lksh -mksh
app-alternatives/tar-0:0 gnu -libarchive split-usr
app-alternatives/yacc-1-r2:0 bison -byacc -reference
app-arch/bzip2-1.0.8-r4:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs -verify-sig
app-arch/cpio-2.15:0 nls
app-arch/gzip-1.13:0 -pic -static -verify-sig
app-arch/libarchive-3.7.2:0/13 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -blake2 bzip2 e2fsprogs -expat iconv -lz4 lzma -lzo -nettle -static-libs -verify-sig xattr -zstd
app-arch/tar-1.35:0 acl -minimal nls -selinux -verify-sig xattr
app-arch/unzip-6.0_p27-r1:0 bzip2 -natspec unicode
app-arch/xz-utils-5.4.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc extra-filters nls -pgo split-usr -static-libs -verify-sig
app-arch/zstd-1.5.5:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -lz4 lzma split-usr -static-libs -test zlib
app-crypt/gnupg-2.4.4:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server
app-crypt/gpgme-1.23.2:1/11.6.15.2 -common-lisp cxx debug -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -qt5 -qt6 -static-libs -test -verify-sig
app-crypt/libb2-0.98.1-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -native-cflags openmp -static-libs
app-crypt/libmd-1.1.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
app-crypt/pinentry-1.2.1-r4:0 -X -caps -efl -emacs -gtk -keyring ncurses -qt5 -verify-sig -wayland
app-crypt/rhash-1.4.4-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug nls ssl -static-libs
app-editors/nano-7.2-r1:0 -debug -justify -magic -minimal ncurses nls spell -static unicode
app-eselect/eselect-fontconfig-20220403:0
app-eselect/eselect-iptables-20220320:0
app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0
app-eselect/eselect-pinentry-0.7.3:0
app-i18n/man-pages-ja-20180315-r1:0
app-i18n/man-pages-l10n-4.19.0:0 l10n_cs l10n_da l10n_de l10n_el l10n_es l10n_fi l10n_fr l10n_hu l10n_id l10n_it l10n_mk l10n_nb l10n_nl l10n_pl l10n_pt-BR l10n_ro l10n_ru l10n_sr l10n_sv l10n_uk l10n_vi
app-i18n/man-pages-zh_CN-1.6.4.0:0
app-misc/ca-certificates-20230311.3.96.1:0 -cacert
app-misc/editor-wrapper-4-r1:0
app-misc/mime-types-2.1.54:0 -nginx
app-misc/pax-utils-1.3.7:0 -caps -man -python -python_single_target_python3_10 python_single_target_python3_11 -seccomp -test
app-misc/tmux-3.3a-r1:0 debug -selinux -systemd -utempter -vim-syntax
app-portage/eix-0.36.7:0 debug -doc nls -sqlite
app-portage/elt-patches-20240116:0
app-portage/gemato-20.5:0 gpg -pretty-log python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test -tools
app-portage/gentoolkit-0.6.5:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
app-portage/getuto-1.9.1:0 -test
app-portage/portage-utils-0.96.1:0 openmp qmanifest qtegrity -static
app-shells/bash-5.2_p26:0 -afs -bashlogger -examples -mem-scramble net nls -pgo -plugins readline -verify-sig
app-shells/bash-completion-2.11:0 eselect -test
app-shells/gentoo-bashcomp-20230313:0
app-shells/push-3.4:0
app-shells/quoter-4.2:0
app-text/ansifilter-2.20:0 -gui -verify-sig
app-text/asciidoc-10.2.0:0 -python_single_target_pypy3 -python_single_target_python3_10 python_single_target_python3_11 -python_single_target_python3_12
app-text/build-docbook-catalog-2.4:0
app-text/docbook-xml-dtd-4.5-r2:4.5
app-text/docbook-xml-dtd-4.4-r3:4.4
app-text/docbook-xml-dtd-4.2-r3:4.2
app-text/docbook-xml-dtd-4.1.2-r7:4.1.2
app-text/docbook-xsl-ns-stylesheets-1.79.1:0 -ruby
app-text/docbook-xsl-stylesheets-1.79.1-r4:0 -ruby
app-text/manpager-1:0
app-text/opensp-1.5.2-r10:0 -doc nls -static-libs -test
app-text/po4a-0.69:0 -test -test
app-text/sgml-common-0.6.3-r7:0
app-text/xmlto-0.0.28-r11:0 -latex text
dev-build/autoconf-2.72-r1:2.72 -emacs -verify-sig
dev-build/autoconf-archive-2023.02.20:0
dev-build/autoconf-wrapper-20231224:0
dev-build/automake-1.16.5-r1:1.16 -test
dev-build/automake-wrapper-20221207:0
dev-build/cmake-3.28.1-r1:0 -dap -doc -gui ncurses -qt6 -test -test -verify-sig
dev-build/gtk-doc-am-1.33.2:0
dev-build/libtool-2.4.7-r2:2 -vanilla
dev-build/make-4.4.1-r1:0 -guile nls -static -verify-sig
dev-build/meson-1.3.1-r1:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test -verify-sig
dev-build/meson-format-array-0:0 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
dev-build/ninja-1.11.1-r4:0 -doc -test
dev-db/sqlite-3.44.2-r2:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug -doc -icu readline -secure-delete -static-libs -tcl -test -tools
dev-lang/duktape-2.7.0-r3:0/2.7.0
dev-lang/perl-5.38.2-r1:0/5.38 -berkdb debug -doc gdbm ithreads -minimal -quadmath
dev-lang/python-3.12.1_p1:3.12 -bluetooth -build debug ensurepip -examples gdbm -libedit ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig
dev-lang/python-3.11.7:3.11 -bluetooth -build debug ensurepip -examples gdbm -libedit ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig
dev-lang/python-3.10.13:3.10 -bluetooth -build debug ensurepip -examples gdbm -libedit ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml
dev-lang/python-exec-2.4.10:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-lang/python-exec-conf-2.4.6:2 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
dev-lang/swig-4.2.0:0 -ccache -doc pcre -test
dev-lang/tcl-8.6.13-r1:0/8.6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug threads
dev-libs/boehm-gc-8.2.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx large -static-libs threads
dev-libs/elfutils-0.190:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -debuginfod -lzma nls -static-libs -test utils -verify-sig -zstd
dev-libs/expat-2.5.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples -static-libs -test unicode
dev-libs/glib-2.78.4-r1:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -dbus debug elf -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr
dev-libs/gmp-6.3.0-r1:0/10.4 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpudetection cxx -doc -pic -static-libs
dev-libs/gobject-introspection-1.78.1:0 -doctool -gtk-doc -python_single_target_python3_10 python_single_target_python3_11 -test
dev-libs/gobject-introspection-common-1.78.1:0
dev-libs/isl-0.26:0/23 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/jsoncpp-1.9.5:0/25 -doc -test
dev-libs/libassuan-2.5.6:0 -verify-sig
dev-libs/libatomic_ops-7.8.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32
dev-libs/libbsd-0.11.8:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -verify-sig
dev-libs/libevent-2.1.12-r1:0/2.1-7 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 clock-gettime debug -malloc-replacement ssl -static-libs -test -verbose-debug -verify-sig
dev-libs/libffi-3.4.4-r4:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug -exec-static-trampoline -pax-kernel -static-libs -test
dev-libs/libgcrypt-1.10.3-r1:0/20 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_aes -cpu_flags_arm_neon -cpu_flags_arm_sha1 -cpu_flags_arm_sha2 -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx2 -cpu_flags_ppc_vsx3 cpu_flags_x86_aes cpu_flags_x86_avx cpu_flags_x86_avx2 -cpu_flags_x86_padlock -cpu_flags_x86_sha cpu_flags_x86_sse4_1 -doc getentropy -static-libs -verify-sig
dev-libs/libgpg-error-1.47-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -common-lisp nls -static-libs -test -verify-sig
dev-libs/libksba-1.6.5:0 -static-libs -verify-sig
dev-libs/libpcre2-10.42-r1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 jit -libedit pcre16 pcre32 readline split-usr -static-libs unicode -valgrind -verify-sig zlib
dev-libs/libpipeline-1.5.7:0 -test
dev-libs/libtasn1-4.19.0:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -test -verify-sig
dev-libs/libunistring-1.1-r1:0/5 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -static-libs
dev-libs/libuv-1.47.0-r1:0/1
dev-libs/libxml2-2.12.4:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -examples ftp -icu -lzma python python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 readline -static-libs -test
dev-libs/libxslt-1.1.39:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 crypt debug -examples -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -static-libs
dev-libs/lzo-2.10:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples split-usr -static-libs
dev-libs/mpc-1.3.1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/mpfr-4.2.1:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -verify-sig
dev-libs/nettle-3.9.1:0/8-6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_aes -cpu_flags_arm_neon -cpu_flags_arm_sha1 -cpu_flags_arm_sha2 -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx2 -cpu_flags_ppc_vsx3 cpu_flags_x86_aes cpu_flags_x86_pclmul -cpu_flags_x86_sha -doc gmp -static-libs -verify-sig
dev-libs/npth-1.6-r2:0 -test
dev-libs/openssl-3.1.4:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpu_flags_x86_sse2 -fips -ktls -rfc3779 -sctp -static-libs -test -tls-compression -vanilla -verify-sig -verify-sig -weak-ssl-ciphers
dev-libs/popt-1.19-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static-libs
dev-perl/Encode-EUCJPASCII-0.30.0-r1:0 -test
dev-perl/Encode-HanExtra-0.230.0-r3:0
dev-perl/Encode-Locale-1.50.0-r1:0 -test
dev-perl/ExtUtils-CChecker-0.110.0:0 -test
dev-perl/File-BaseDir-0.90.0:0 -test
dev-perl/File-DesktopEntry-0.220.0-r1:0 -test
dev-perl/File-MimeInfo-0.330.0:0 -test
dev-perl/IO-Socket-SSL-2.83.0:0 -examples -idn -test
dev-perl/IPC-System-Simple-1.300.0:0 -test
dev-perl/Locale-gettext-1.70.0-r1:0 -test
dev-perl/MIME-Charset-1.13.1:0 l10n_ja l10n_zh -test
dev-perl/Module-Build-0.423.400:0 -test
dev-perl/Mozilla-CA-20999999-r1:0 -test
dev-perl/Net-SSLeay-1.920.0-r1:0 -examples -examples -minimal -test
dev-perl/Pod-Parser-1.660.0:0 -test
dev-perl/Regexp-IPv6-0.30.0-r2:0 -test
dev-perl/SGMLSpm-1.1-r2:0 -test
dev-perl/Syntax-Keyword-Try-0.280.0:0 -test
dev-perl/TermReadKey-2.380.0-r1:0 -examples -test
dev-perl/Text-CharWidth-0.40.0-r2:0 -test
dev-perl/Text-WrapI18N-0.60.0-r2:0 -test
dev-perl/Unicode-LineBreak-2019.1.0:0
dev-perl/URI-5.210.0:0 -test
dev-perl/XS-Parse-Keyword-0.380.0:0 -test
dev-perl/YAML-Tiny-1.740.0:0 -minimal -test
dev-python/certifi-3021.3.16-r4:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/charset-normalizer-3.3.2:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/cython-3.0.8:0 debug -doc python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/editables-0.5:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/ensurepip-pip-23.3.2:0
dev-python/ensurepip-setuptools-69.0.3:0
dev-python/ensurepip-wheels-100:0
dev-python/flit-core-3.9.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/gentoo-common-1:0
dev-python/gpep517-15:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/hatchling-1.21.1:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/idna-3.6:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/installer-0.7.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/jaraco-context-4.3.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/jaraco-functools-4.0.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/jaraco-text-3.12.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/jinja-3.1.3:0 -doc -examples python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/lxml-5.1.0:0 debug -doc -examples python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test threads
dev-python/markupsafe-2.1.4:0 debug python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/more-itertools-10.2.0:0 -doc python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/nspektr-0.5.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/ordered-set-4.1.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/packaging-23.2:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/pathspec-0.12.1:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/platformdirs-4.1.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/pluggy-1.4.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/pyparsing-3.1.1:0 -examples python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/pypy3-7.3.15:0/pypy310-pp73-384 gdbm ncurses sqlite -tk
dev-python/pypy3_10-7.3.15:0/pypy310-pp73-384 ensurepip gdbm jit ncurses sqlite -tk
dev-python/pypy3_10-exe-bin-7.3.15:7.3.15
dev-python/PySocks-1.7.1-r2:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
dev-python/requests-2.31.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -socks5 -test test-rust
dev-python/setuptools-69.0.3:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/setuptools-scm-8.0.4:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/tomli-2.0.1-r1:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/trove-classifiers-2024.1.8:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/typing-extensions-4.9.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-python/urllib3-2.1.0:0 -brotli python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test -zstd
dev-python/wheel-0.42.0:0 python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 -test
dev-util/checkbashisms-2.23.5:0
dev-util/desktop-file-utils-0.27-r1:0
dev-util/glib-utils-2.78.4:0 -python_single_target_python3_10 python_single_target_python3_11 -python_single_target_python3_12
dev-util/gperf-3.1-r2:0
dev-util/pkgconf-2.1.0-r1:0/4 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -test
dev-util/re2c-3.1:0 debug -test
dev-vcs/git-2.43.0:0 blksha1 -cgi curl -cvs -doc gpg -highlight iconv -keyring -mediawiki nls pcre -perforce -perl -python_single_target_python3_10 python_single_target_python3_11 -python_single_target_python3_12 safe-directory -selinux -subversion -test -tk webdav -xinetd
media-fonts/liberation-fonts-2.1.5:0 -X -X -fontforge
media-gfx/graphite2-1.3.14_p20210810-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -perl -test
media-libs/fontconfig-2.15.0:1.0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc nls -test
media-libs/freetype-2.13.2:2 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 adobe-cff -brotli bzip2 cleartype-hinting debug -doc -fontforge harfbuzz png -static-libs -svg -utils
media-libs/harfbuzz-8.3.0:0/6.0.0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cairo debug -doc -experimental glib graphite -icu introspection -test truetype
media-libs/libpng-1.6.41:0/16 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -apng -cpu_flags_arm_neon cpu_flags_x86_sse -static-libs -test
net-dns/c-ares-1.25.0-r1:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -test -verify-sig
net-dns/libidn2-2.3.7:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static-libs -verify-sig
net-firewall/iptables-1.8.10:0/1.8.3 -conntrack -netlink -nftables -pcap split-usr -static-libs
net-libs/gnutls-3.8.3:0/30.30 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -brotli cxx -dane -doc -examples idn nls openssl -pkcs11 seccomp -sslv2 -sslv3 -static-libs -test -test-full tls-heartbeat -tools -verify-sig zlib -zstd
net-libs/libmnl-1.0.5:0/0.2.0 -examples -verify-sig
net-libs/libnsl-2.0.1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
net-libs/libpsl-0.21.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -icu idn -test
net-libs/libtirpc-1.3.4-r1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -kerberos split-usr -static-libs
net-libs/nghttp2-1.59.0:0/1.14 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug -hpack-tools -jemalloc -static-libs -systemd -test -utils -xml
net-misc/curl-8.5.0-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 adns alt-svc -brotli -curl_ssl_gnutls -curl_ssl_mbedtls curl_ssl_openssl -curl_ssl_rustls ftp -gnutls -gopher hsts http2 -idn imap -kerberos -ldap -mbedtls -nghttp3 openssl pop3 progress-meter psl -rtmp -rustls -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -verify-sig -websockets -zstd
net-misc/dhcpcd-10.0.6-r1:0 debug embedded ipv6 -privsep udev
net-misc/iputils-20231222:0 arping -caps -clockdiff -doc filecaps -idn nls -test -tracepath
net-misc/netifrc-0.7.8:0 dhcp
net-misc/openssh-contrib-9.5_p1:0 -X -X509 -abi_mips_n32 -audit debug -hpn -kerberos -ldns -libedit -livecd pam -pie -security-key -selinux ssl -static -test -verify-sig -xmss
net-misc/rsync-3.2.7-r4:0 acl -examples iconv -lz4 -python_single_target_python3_10 python_single_target_python3_11 -rrsync ssl -stunnel -system-zlib -verify-sig xattr -xxhash -zstd
net-misc/wget-1.21.4:0 -cookie-check debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid -verify-sig zlib
perl-core/File-Temp-0.231.100:0
perl-core/Math-BigInt-1.999.842:0 -examples -test
sec-keys/openpgp-keys-gentoo-release-20230329:0 -test
sys-apps/acl-2.3.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls split-usr -static-libs
sys-apps/attr-2.5.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug nls split-usr -static-libs
sys-apps/baselayout-2.14-r1:0 -build split-usr
sys-apps/coreutils-9.4:0 acl -caps -gmp -hostname -kill -multicall nls openssl -selinux split-usr -static -test -vanilla -verify-sig xattr
sys-apps/dbus-1.15.8:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug -doc elogind -selinux -static-libs -systemd -test -test -valgrind
sys-apps/debianutils-5.14:0 installkernel -static
sys-apps/diffutils-3.10:0 nls -verify-sig
sys-apps/file-5.45-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzip -lzma -python python_targets_python3_10 python_targets_python3_11 -seccomp -static-libs -verify-sig zlib -zstd
sys-apps/findutils-4.9.0-r2:0 nls -selinux -static -test -verify-sig
sys-apps/gawk-5.3.0-r1:0 -mpfr nls -pma readline -verify-sig
sys-apps/gentoo-functions-0.19:0
sys-apps/grep-3.11:0 egrep-fgrep nls pcre -static -verify-sig
sys-apps/groff-1.23.0:0 -X -examples -uchardet
sys-apps/help2man-1.49.3:0 nls
sys-apps/install-xattr-0.8-r1:0
sys-apps/iproute2-6.6.0-r3:0 -atm -berkdb -bpf -caps -elf iptables -minimal -nfs -selinux
sys-apps/kbd-2.6.4:0 nls pam -selinux -test
sys-apps/kmod-31:0 debug -doc lzma -pkcs7 -python python_targets_python3_10 python_targets_python3_11 -static-libs tools zlib zstd
sys-apps/less-643-r1:0 pcre -test
sys-apps/locale-gen-2.23-r1:0
sys-apps/man-db-2.12.0:0 manpager nls seccomp -selinux -static-libs zlib
sys-apps/man-pages-6.05.01:0 l10n_cs l10n_da l10n_de l10n_el l10n_es l10n_fi l10n_fr l10n_hu l10n_id l10n_it l10n_ja l10n_mk l10n_nb l10n_nl l10n_pl l10n_pt-BR l10n_ro l10n_ru l10n_sr l10n_sv l10n_uk l10n_vi l10n_zh-CN
sys-apps/miscfiles-1.5-r4:0 -minimal
sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static
sys-apps/openrc-0.53:0 -audit -bash debug ncurses netifrc -newnet pam -s6 -selinux -sysv-utils sysvinit unicode
sys-apps/portage-3.0.61-r1:0 -apidoc -build -doc -gentoo-dev ipc native-extensions python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12 rsync-verify -selinux -test xattr
sys-apps/sandbox-2.38:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 nnp
sys-apps/sed-4.9:0 acl nls -selinux -static -verify-sig
sys-apps/shadow-4.14.3:0/4 acl -audit -cracklib nls pam -selinux -skey split-usr -su -systemd -verify-sig xattr
sys-apps/systemd-utils-254.9:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -boot -kernel-install kmod -python_single_target_python3_10 python_single_target_python3_11 -python_single_target_python3_12 -secureboot -selinux split-usr -split-usr -sysusers -test tmpfiles udev -ukify
sys-apps/sysvinit-3.08:0 -ibm nls -selinux -static -verify-sig
sys-apps/texinfo-7.1-r1:0 nls standalone -static
sys-apps/util-linux-2.39.3-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -build -caps cramfs -cryptsetup -fdformat hardlink -kill logger -magic ncurses nls pam -python python_targets_python3_10 python_targets_python3_11 readline -rtas -selinux -slang split-usr -static-libs su suid -systemd -test -tty-helpers -udev unicode -verify-sig
sys-apps/which-2.21:0
sys-auth/elogind-252.9:0 acl -audit cgroup-hybrid debug -doc pam policykit -selinux -test
sys-auth/pambase-20240128:0 -caps -debug elogind -gnome-keyring -homed -minimal -mktemp nullok -pam_krb5 -pam_ssh passwdqc -pwhistory -pwquality -securetty -selinux sha512 -sssd -systemd -yescrypt
sys-auth/passwdqc-2.0.3-r1:0
sys-auth/polkit-124-r1:0 daemon duktape -examples -gtk introspection -kde pam -selinux -systemd -test
sys-devel/bc-1.07.1-r6:0 -libedit readline -static
sys-devel/binutils-2.41-r5:2.41 -cet -debuginfod -doc -gold -gprofng -hardened -multitarget nls -pgo plugins -static-libs -test -vanilla -zstd
sys-devel/binutils-config-5.5:0 native-symlinks
sys-devel/bison-3.8.2-r2:0 -examples nls -static -test -verify-sig
sys-devel/flex-2.6.4-r6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static -test
sys-devel/gcc-14.0.0_pre20231217:14 -ada -cet -custom-cflags cxx -d -debug -default-stack-clash-protection -default-znow -doc -fixed-point fortran -go graphite -hardened -ieee-long-double -jit -libssp lto -modula2 multilib nls -objc -objc++ -objc-gc openmp -pch -pgo pie -rust sanitize ssp -systemtap -test -valgrind -vanilla -vtv -zstd
sys-devel/gcc-config-2.11:0 cc-wrappers native-symlinks
sys-devel/gettext-0.22.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl cxx -doc -emacs -git -java -java ncurses nls openmp -static-libs -verify-sig xattr
sys-devel/gnuconfig-20230731:0
sys-devel/m4-1.4.19-r2:0 -examples nls -verify-sig
sys-devel/patch-2.7.6-r5:0 -static -test -verify-sig xattr
sys-fs/e2fsprogs-1.47.0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cron -fuse nls split-usr -static-libs -test tools
sys-fs/udev-init-scripts-35:0
sys-kernel/dracut-060_pre20240104:0 -selinux -test
sys-kernel/gentoo-kernel-bin-6.1.75:6.1.75 initramfs -test
sys-kernel/installkernel-19:0 dracut -grub -systemd -uki -ukify
sys-kernel/linux-headers-6.7:0 -headers-only
sys-libs/gdbm-1.23:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 berkdb nls readline -static-libs -test -verify-sig
sys-libs/glibc-2.38-r9:2.2 -audit -caps -cet -compile-locales -crypt -custom-cflags -doc -gd -hash-sysv-compat -headers-only multiarch multilib -multilib-bootstrap -nscd -perl -profile -selinux ssp stack-realign static-libs -suid -systemd -systemtap -test -vanilla
sys-libs/libcap-2.69:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 pam split-usr -static-libs -tools
sys-libs/libseccomp-2.5.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -experimental-loong -python python_targets_python3_10 python_targets_python3_11 -static-libs -test
sys-libs/libxcrypt-4.4.36-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 compat -headers-only split-usr -static-libs system -test
sys-libs/ncurses-6.4_p20230401:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -ada cxx debug -doc -gpm -minimal -profile split-usr -split-usr stack-realign -static-libs -test tinfo -trace -verify-sig
sys-libs/pam-1.5.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -berkdb -debug filecaps -nis -selinux split-usr
sys-libs/readline-8.2_p10:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static-libs unicode -utils -verify-sig
sys-libs/timezone-data-2023d:0 -leaps-timezone nls -zic-slim
sys-libs/zlib-1.3.1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 minizip split-usr -static-libs -verify-sig
sys-process/procps-4.0.4:0/0-ng -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 elogind kill -modern-top ncurses nls -selinux split-usr -static-libs -systemd -test unicode
sys-process/psmisc-23.6:0 -X -apparmor nls -selinux -test
virtual/acl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
virtual/dev-manager-0-r2:0
virtual/dist-kernel-6.1.75:0/6.1.75
virtual/editor-0-r7:0
virtual/libc-1-r1:0
virtual/libcrypt-2-r1:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
virtual/libelf-3-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libiconv-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libintl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libudev-251-r2:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -systemd
virtual/man-0-r4:0
virtual/openssh-0:0 ssl
virtual/os-headers-0-r2:0
virtual/package-manager-1:0
virtual/pager-0-r1:0
virtual/perl-bignum-0.660.0:0
virtual/perl-Carp-1.540.0:0
virtual/perl-CPAN-2.360.0:0
virtual/perl-CPAN-Meta-2.150.10-r7:0
virtual/perl-CPAN-Meta-YAML-0.18.0-r9:0
virtual/perl-Data-Dumper-2.188.0:0
virtual/perl-Encode-3.190.0:0
virtual/perl-Exporter-5.770.0-r1:0
virtual/perl-ExtUtils-CBuilder-0.280.238:0
virtual/perl-ExtUtils-Install-2.220.0:0
virtual/perl-ExtUtils-MakeMaker-7.700.0:0
virtual/perl-ExtUtils-Manifest-1.730.0-r2:0
virtual/perl-ExtUtils-ParseXS-3.510.0:0
virtual/perl-File-Path-2.180.0-r2:0
virtual/perl-File-Spec-3.880.0:0
virtual/perl-File-Temp-0.231.100:0
virtual/perl-Getopt-Long-2.540.0:0
virtual/perl-JSON-PP-4.160.0-r1:0
virtual/perl-libnet-3.150.0:0 ssl
virtual/perl-Math-BigInt-1.999.842:0
virtual/perl-Math-BigInt-FastCalc-0.501.300:0
virtual/perl-Math-BigRat-0.262.400:0
virtual/perl-Math-Complex-1.620.0:0
virtual/perl-MIME-Base64-3.160.100_rc:0
virtual/perl-Module-Metadata-1.0.37-r3:0
virtual/perl-parent-0.241.0:0
virtual/perl-Parse-CPAN-Meta-2.150.10-r7:0
virtual/perl-Perl-OSType-1.10.0-r7:0
virtual/perl-podlators-5.10.0:0
virtual/perl-Scalar-List-Utils-1.630.0:0
virtual/perl-Test-Harness-3.440.0-r1:0
virtual/perl-Text-ParseWords-3.310.0-r1:0
virtual/perl-Unicode-Collate-1.310.0-r1:0
virtual/perl-version-0.992.900-r1:0
virtual/pkgconfig-2-r1:0
virtual/service-manager-1-r1:0
virtual/ssh-0-r2:0 -minimal
virtual/tmpfiles-0-r5:0 -systemd
virtual/ttf-fonts-1-r2:0
virtual/udev-217-r7:0 -systemd
virtual/w3m-1:0
www-client/pybugz-0.13-r2:0 python_targets_python3_10 python_targets_python3_11
www-client/w3m-0.5.3_p20230121:0 -X -fbcon -gdk-pixbuf -gpm -imlib l10n_ja -lynxkeymap nls -nntp ssl unicode -xface
x11-apps/xprop-1.2.6:0
x11-apps/xset-1.2.5:0
x11-base/xcb-proto-1.16.0:0 python_targets_python3_10 python_targets_python3_11 python_targets_python3_12
x11-base/xorg-proto-2023.2:0 -test
x11-libs/cairo-1.18.0:0 X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug glib -gtk-doc -test
x11-libs/libICE-1.1.1-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
x11-libs/libSM-1.2.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc uuid
x11-libs/libX11-1.8.7:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -test
x11-libs/libXau-1.0.11:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc
x11-libs/libxcb-1.16-r1:0/1.12 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -doc -selinux -test xkb
x11-libs/libXdmcp-1.1.4-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc
x11-libs/libXext-1.3.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc
x11-libs/libXmu-1.1.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc
x11-libs/libXrender-0.9.11:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
x11-libs/libXt-1.3.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -test
x11-libs/pixman-0.43.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs -test
x11-libs/xtrans-1.5.0:0 -doc
x11-misc/compose-tables-1.8.7:0
x11-misc/shared-mime-info-2.4:0 -test
x11-misc/util-macros-1.20.0:0
x11-misc/xdg-utils-1.2.0_beta1_p20231203:0 -dbus -doc -gnome


#############
# build.log #
#############


>>> Unpacking source...
>>> Unpacking modeller-9.25.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.25/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.25/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
/usr/lib/python-exec/python3.12/2to3:3: DeprecationWarning: lib2to3 package is deprecated and may not be able to parse Python 3.10+
  from lib2to3.main import main
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored modlib/modeller/__init__.py
--- modlib/modeller/__init__.py	(original)
+++ modlib/modeller/__init__.py	(refactored)
@@ -48,7 +48,7 @@
         return sys.maxsize > 2**32
     # This works on older Pythons, but not in Python 3
     else:
-        return type(sys.dllhandle) == long
+        return type(sys.dllhandle) == int
 
 # Special processing on Windows to find _modeller.pyd and Modeller DLLs:
 if hasattr(config, 'install_dir') and hasattr(sys, 'dllhandle'):
RefactoringTool: No changes to modlib/modeller/alignment.py
RefactoringTool: No changes to modlib/modeller/alnsequence.py
RefactoringTool: No changes to modlib/modeller/alnstructure.py
RefactoringTool: No changes to modlib/modeller/atom_type.py
RefactoringTool: Refactored modlib/modeller/coordinates.py
--- modlib/modeller/coordinates.py	(original)
+++ modlib/modeller/coordinates.py	(refactored)
@@ -147,7 +147,7 @@
         (startres, endres) = self._get_resind()
         (startatm, endatm) = get_residue_atom_indices(self.seq, startres,
                                                       endres)
-        return (range(startatm+1, endatm+1), self.seq)
+        return (list(range(startatm+1, endatm+1)), self.seq)
 
     atoms = property(__get_atoms, doc="List of all atoms in this chain")
 
@@ -158,7 +158,7 @@
     def get_atom_indices(self):
         (startind, endind) = get_residue_atom_indices(self.mdl, self._num,
                                                       self._num + 1)
-        return range(startind + 1, endind + 1), self.mdl
+        return list(range(startind + 1, endind + 1)), self.mdl
 
     def __repr__(self):
         # Get residue number before we do anything else. For alignment
@@ -252,7 +252,7 @@
     def get_atom_indices(self):
         (startind, endind) = get_residue_atom_indices(self.mdl, self.offset,
                                                       self.offset + len(self))
-        return range(startind + 1, endind + 1), self.mdl
+        return list(range(startind + 1, endind + 1)), self.mdl
 
     def __getitem__(self, indx):
         ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres,
@@ -398,7 +398,7 @@
             return self.mdl.natm
 
     def get_atom_indices(self):
-        return range(self.offset + 1, self.offset + len(self) + 1), self.mdl
+        return list(range(self.offset + 1, self.offset + len(self) + 1)), self.mdl
 
     def __getitem__(self, indx):
         ret = modutil.handle_seq_indx(self, indx, self.mdl._indxatm,
RefactoringTool: No changes to modlib/modeller/density.py
RefactoringTool: No changes to modlib/modeller/energy_data.py
RefactoringTool: No changes to modlib/modeller/energy_profile.py
RefactoringTool: No changes to modlib/modeller/environ.py
RefactoringTool: No changes to modlib/modeller/excluded_pair.py
RefactoringTool: No changes to modlib/modeller/excluded_pair_list.py
RefactoringTool: No changes to modlib/modeller/features.py
RefactoringTool: No changes to modlib/modeller/forms.py
RefactoringTool: No changes to modlib/modeller/gbsa.py
RefactoringTool: No changes to modlib/modeller/group_restraints.py
RefactoringTool: Refactored modlib/modeller/id_table.py
--- modlib/modeller/id_table.py	(original)
+++ modlib/modeller/id_table.py	(refactored)
@@ -40,7 +40,7 @@
 def write_seqid_matrix(fh, coder, mat):
     """Write a sequence identity matrix to a file"""
     nseq = len(mat)
-    print(" " * 9 + "".join([ s[:8] for s in coder ]))
+    print((" " * 9 + "".join([ s[:8] for s in coder ])))
     for n1 in range(nseq):
         fh.write(coder[n1][:8] + " " + \
                  "".join(["%8d" % (mat[n1][n2]+0.5) for n2 in range(nseq)]))
RefactoringTool: No changes to modlib/modeller/information.py
RefactoringTool: No changes to modlib/modeller/io_data.py
RefactoringTool: Refactored modlib/modeller/libraries.py
--- modlib/modeller/libraries.py	(original)
+++ modlib/modeller/libraries.py	(refactored)
@@ -32,7 +32,7 @@
             return BytesIO(*args)
     else:
         def _make_bytes_io(self, *args):
-            from cStringIO import StringIO
+            from io import StringIO
             return StringIO(*args)
 
     def __getstate__(self):
RefactoringTool: Refactored modlib/modeller/model.py
--- modlib/modeller/model.py	(original)
+++ modlib/modeller/model.py	(refactored)
@@ -121,7 +121,7 @@
 
     def get_atom_indices(self):
         """Get the indices of all atoms in this model"""
-        return (range(1, self.natm+1), self)
+        return (list(range(1, self.natm+1)), self)
 
     def read(self, file, model_format='PDB',
              model_segment=('FIRST:@', 'LAST:'), io=None,
@@ -340,7 +340,7 @@
         dope_score = sel.assess_dope()
         scorer = normalized_dope.DOPEScorer(self)
         z_score = scorer.get_z_score(dope_score)
-        print(">> Normalized DOPE z score: %.3f" % z_score)
+        print((">> Normalized DOPE z score: %.3f" % z_score))
         return z_score
 
     def assess_normalized_dopehr(self):
@@ -351,7 +351,7 @@
         dope_score = sel.assess_dopehr()
         scorer = normalized_dope.DOPEHRScorer(self)
         z_score = scorer.get_z_score(dope_score)
-        print(">> Normalized DOPE-HR z score: %.3f" % z_score)
+        print((">> Normalized DOPE-HR z score: %.3f" % z_score))
         return z_score
 
     def get_normalized_dope_profile(self):
RefactoringTool: Refactored modlib/modeller/model_topology.py
--- modlib/modeller/model_topology.py	(original)
+++ modlib/modeller/model_topology.py	(refactored)
@@ -50,7 +50,7 @@
         self.check_args = args
     def __iter__(self):
         return self
-    def next(self):
+    def __next__(self):
         while True:
             atoms = self.__int_next()
             if self.check_func is None \
@@ -82,7 +82,7 @@
         self.check_args = args
     def __iter__(self):
         return self
-    def next(self):
+    def __next__(self):
         while True:
             atoms = self.__int_next()
             if self.check_func is None \
RefactoringTool: No changes to modlib/modeller/modfile.py
RefactoringTool: No changes to modlib/modeller/normalized_dope.py
RefactoringTool: No changes to modlib/modeller/orient.py
RefactoringTool: No changes to modlib/modeller/parameters.py
RefactoringTool: Refactored modlib/modeller/physical.py
--- modlib/modeller/physical.py	(original)
+++ modlib/modeller/physical.py	(refactored)
@@ -31,7 +31,7 @@
     def __init__(self, default=1.0, **keys):
         self._default = default
         self._dict = {}
-        for (term,val) in keys.items():
+        for (term,val) in list(keys.items()):
             term = eval("%s" % term)
             self[term] = val
 
RefactoringTool: No changes to modlib/modeller/profile.py
RefactoringTool: No changes to modlib/modeller/pseudo_atom.py
RefactoringTool: No changes to modlib/modeller/pseudo_atom_list.py
RefactoringTool: No changes to modlib/modeller/pssmdb.py
RefactoringTool: No changes to modlib/modeller/residue.py
RefactoringTool: No changes to modlib/modeller/restraints.py
RefactoringTool: No changes to modlib/modeller/rigid_body.py
RefactoringTool: No changes to modlib/modeller/rigid_body_list.py
RefactoringTool: Refactored modlib/modeller/salign.py
--- modlib/modeller/salign.py	(original)
+++ modlib/modeller/salign.py	(refactored)
@@ -38,8 +38,8 @@
             return aln.salign(auto_overhang=True, overhang_auto_limit=5,
                               overhang_factor=1, **keys)
         except modeller.ModellerError:
-            print("SALIGN with auto_overhang failed: %s" \
-                  % str(sys.exc_info()[1]))
+            print(("SALIGN with auto_overhang failed: %s" \
+                  % str(sys.exc_info()[1])))
             print("Retrying without auto_overhang")
             return aln.salign(**keys)
 
@@ -118,13 +118,13 @@
                 self.qscore = res.qscorepct
                 self.aln.write(file=output_aln_file, alignment_format='PIR')
                 better = True
-            print("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty,
-                                            res.qscorepct))
+            print(("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty,
+                                            res.qscorepct)))
         except modeller.ModellerError:
-            print("Set of parameters %s %g %g resulted in the "
+            print(("Set of parameters %s %g %g resulted in the "
                   "following error\t%s" % (str(weights), open_penalty,
                                            extend_penalty,
-                                           str(sys.exc_info()[1])))
+                                           str(sys.exc_info()[1]))))
         return better
 
 
@@ -181,7 +181,7 @@
                 best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d,
                                      align_block)
 
-    print("final max quality = %g" % best.qscore)
+    print(("final max quality = %g" % best.qscore))
 
     if best.found_struc_align:
         aln.clear()
RefactoringTool: Refactored modlib/modeller/saxsdata.py
--- modlib/modeller/saxsdata.py	(original)
+++ modlib/modeller/saxsdata.py	(refactored)
@@ -206,7 +206,7 @@
         try:
             fh = open(saxsfilename,'r')
         except:
-            print("file "+saxsfilename+" not found :(")
+            print(("file "+saxsfilename+" not found :("))
             return
         fh.close()
         ns = 0
@@ -225,8 +225,8 @@
             s_low = s_min - .001
         if (not s_hi):
             s_hi = s_max + .001
-        print("s_min=%s, s_max=%s" % (str(s_min), str(s_max)))
-        print("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi)))
+        print(("s_min=%s, s_max=%s" % (str(s_min), str(s_max))))
+        print(("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi))))
         self.ini_saxs(atmsel,
                  filename=formfacfilename,
                  s_min=s_min, s_max=s_max, maxs=ns, nmesh=ns, natomtyp=natomtyp,
RefactoringTool: No changes to modlib/modeller/schedule.py
RefactoringTool: No changes to modlib/modeller/secondary_structure.py
RefactoringTool: Refactored modlib/modeller/selection.py
--- modlib/modeller/selection.py	(original)
+++ modlib/modeller/selection.py	(refactored)
@@ -23,7 +23,7 @@
             return self.mdl.atoms[obj - 1]
     else:
         def next(self):
-            obj = self.seliter.next()
+            obj = next(self.seliter)
             return self.mdl.atoms[obj - 1]
 
 class selection(object):
@@ -52,7 +52,7 @@
            :rtype: list of ints
         """
         if sys.version_info[:2] == (2,3):
-            keys = self.__selection.keys()
+            keys = list(self.__selection.keys())
             keys.sort()
         else:
             keys = sorted(self.__selection.keys())
@@ -722,9 +722,9 @@
     def assess(self, assessor, output='SHORT NO_REPORT', **vars):
         """Assess with the given assessor object
            (e.g. :class:`soap_loop.Scorer`)."""
-        print(">> Model assessment by %s" % assessor.name)
+        print((">> Model assessment by %s" % assessor.name))
         molpdf, terms = assessor._assess(self, output=output, **vars)
-        print("%s                     : %12.6f" % (assessor.name, molpdf))
+        print(("%s                     : %12.6f" % (assessor.name, molpdf)))
         return molpdf
 
     def _dope_energy(self, gprsr, name, output='SHORT NO_REPORT',
@@ -733,7 +733,7 @@
                                                     nonbond_spline=1.), **vars):
         """Internal function to do DOPE or DOPE-HR assessment"""
         mdl = self.__mdl
-        print(">> Model assessment by %s potential" % name)
+        print((">> Model assessment by %s potential" % name))
         edat = self.get_dope_energy_data()
         old_gprsr = mdl.group_restraints
         mdl.group_restraints = gprsr
@@ -744,7 +744,7 @@
                             **vars)
         finally:
             mdl.group_restraints = old_gprsr
-        print("%s score               : %12.6f" % (name, molpdf))
+        print(("%s score               : %12.6f" % (name, molpdf)))
         return molpdf
 
     def debug_function(self, residue_span_range=(0, 99999),
RefactoringTool: No changes to modlib/modeller/sequence.py
RefactoringTool: No changes to modlib/modeller/sequence_db.py
RefactoringTool: No changes to modlib/modeller/soap_loop.py
RefactoringTool: No changes to modlib/modeller/soap_peptide.py
RefactoringTool: No changes to modlib/modeller/soap_pp.py
RefactoringTool: No changes to modlib/modeller/soap_protein_od.py
RefactoringTool: No changes to modlib/modeller/superpose.py
RefactoringTool: No changes to modlib/modeller/symmetry.py
RefactoringTool: No changes to modlib/modeller/symmetry_list.py
RefactoringTool: No changes to modlib/modeller/terms.py
RefactoringTool: Refactored modlib/modeller/test.py
--- modlib/modeller/test.py	(original)
+++ modlib/modeller/test.py	(refactored)
@@ -2,7 +2,7 @@
 import modeller
 import math
 try:
-    from cStringIO import StringIO
+    from io import StringIO
 except ImportError:
     from io import StringIO
 import sys
@@ -150,7 +150,7 @@
         diff = abs(num1 - num2)
         if msg is None:
             msg = "%f != %f within %g" % (num1, num2, tolerance)
-        self.assert_(diff < tolerance, msg)
+        self.assertTrue(diff < tolerance, msg)
 
     def run_capture_stdout(self, method, *args, **keys):
         """Run a method and capture its standard output. Returns both the
RefactoringTool: No changes to modlib/modeller/topology.py
RefactoringTool: No changes to modlib/modeller/virtual_atom.py
RefactoringTool: No changes to modlib/modeller/automodel/__init__.py
RefactoringTool: No changes to modlib/modeller/automodel/allhmodel.py
RefactoringTool: No changes to modlib/modeller/automodel/assess.py
RefactoringTool: Refactored modlib/modeller/automodel/automodel.py
--- modlib/modeller/automodel/automodel.py	(original)
+++ modlib/modeller/automodel/automodel.py	(refactored)
@@ -203,13 +203,13 @@
 
     def write_ok_summary(self, all, modeltyp):
         """Print out a summary of all successfully generated models"""
-        print("\n>> Summary of successfully produced %s:" % modeltyp)
-        fields = [x for x in all[0].keys() if x.endswith(' score')]
+        print(("\n>> Summary of successfully produced %s:" % modeltyp))
+        fields = [x for x in list(all[0].keys()) if x.endswith(' score')]
         fields.sort()
         fields = ['molpdf'] + fields
         header = '%-25s ' % 'Filename' + " ".join(['%14s' % x for x in fields])
         print(header)
-        print('-' * len(header))
+        print(('-' * len(header)))
         for mdl in all:
             text = '%-25s' % mdl['name']
             for field in fields:
@@ -222,9 +222,9 @@
 
     def write_failure_summary(self, all, modeltyp):
         """Print out a summary of all failed models"""
-        print("\n>> Summary of failed %s:" % modeltyp)
+        print(("\n>> Summary of failed %s:" % modeltyp))
         for mdl in all:
-            print("%-25s %s" % (mdl['name'], mdl['failure']))
+            print(("%-25s %s" % (mdl['name'], mdl['failure'])))
         print('')
 
     def rd_restraints(self):
@@ -692,8 +692,8 @@
         elif atmsel.get_model() is not self:
             raise ModellerError("selection is defined on the wrong model")
         elif len(atmsel) < len(self.atoms):
-            print("%d (of %d total) atoms selected for optimization" \
-                  % (len(atmsel), len(self.atoms)))
+            print(("%d (of %d total) atoms selected for optimization" \
+                  % (len(atmsel), len(self.atoms))))
         return atmsel
 
     def mkhomcsr(self, atmsel, aln):
@@ -774,9 +774,9 @@
         selstd = selection(self).only_std_residues()
         selca = selstd.only_atom_types('CA')
 
-        print("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \
+        print(("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \
               + "to protein atoms within %.2f angstroms\n" % bond_distance \
-              + "and protein CA atoms within %.2f angstroms" % ca_distance)
+              + "and protein CA atoms within %.2f angstroms" % ca_distance))
         # Build the bonds first; this avoids duplicated CA-ligand bonds since
         # make_distance() will not build restraints that are already on the
         # nonbond exclusion list
@@ -823,8 +823,8 @@
         selhet = selhet.only_no_topology()
 
         # Intra-residue:
-        print("%d atoms in residues without defined topology\n" % len(selhet) \
-              + "constrained to be rigid bodies")
+        print(("%d atoms in residues without defined topology\n" % len(selhet) \
+              + "constrained to be rigid bodies"))
         rsr = self.restraints
         rsr.make_distance(selhet, selhet, aln=aln,
                           distance_rsr_model=7, maximal_distance=10.0,
@@ -898,8 +898,8 @@
             print("\nThe following CHARMM atom type assignments were made:")
             print("      Atom                 Old type        New type")
             for atom, old_type, new_type in zip(sel, old_types, new_types):
-                print("      %-20s %-15s %-15s"
-                      % (str(atom), fmt_typ(old_type), fmt_typ(new_type)))
+                print(("      %-20s %-15s %-15s"
+                      % (str(atom), fmt_typ(old_type), fmt_typ(new_type))))
 
     def select_atoms(self):
         """Select atoms to be optimized in the model building procedure. By
RefactoringTool: No changes to modlib/modeller/automodel/autosched.py
RefactoringTool: No changes to modlib/modeller/automodel/dope_loopmodel.py
RefactoringTool: No changes to modlib/modeller/automodel/dopehr_loopmodel.py
RefactoringTool: Refactored modlib/modeller/automodel/generate.py
--- modlib/modeller/automodel/generate.py	(original)
+++ modlib/modeller/automodel/generate.py	(refactored)
@@ -88,11 +88,11 @@
                 to_rebuild.append(r)
                 _unbuild_ring(r, ring_atoms + extra_atoms)
     if len(to_rebuild) > 0:
-        print("The following %d residues contain 6-membered rings with "
+        print(("The following %d residues contain 6-membered rings with "
               "poor geometries\nafter transfer from templates. Rebuilding "
               "rings from internal coordinates:\n   %s" \
               % (len(to_rebuild),
-                 "\n   ".join([str(r) for r in to_rebuild])))
+                 "\n   ".join([str(r) for r in to_rebuild]))))
         mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
 
 def read_xyz(mdl, aln):
RefactoringTool: Refactored modlib/modeller/automodel/loopmodel.py
--- modlib/modeller/automodel/loopmodel.py	(original)
+++ modlib/modeller/automodel/loopmodel.py	(refactored)
@@ -105,7 +105,7 @@
         lendef = len(self._defined_indices)
         if lenall > lendef:
             s = selection(self) - s
-            print("""
+            print(("""
 The following %d atoms were not found in the input model's non-loop region,
 and were added automatically by Modeller in order to determine correct
 interactions between the loop and the rest of the protein:
@@ -115,7 +115,7 @@
 rest of the protein may exist (note, however, that the score of the loop does
 not include protein-protein internal interactions, so will not be adversely
 affected by any clashes).""" \
-% (lenall - lendef, ", ".join([repr(a) for a in s])))
+% (lenall - lendef, ", ".join([repr(a) for a in s]))))
 
             if self.loop.write_defined_only:
                 print("""
@@ -406,7 +406,7 @@
         elif len(atmsel.only_no_topology()) > 0:
             raise ModellerError("some selected residues have no topology")
         else:
-            print("%d atoms selected for loop refinement" % len(atmsel))
+            print(("%d atoms selected for loop refinement" % len(atmsel)))
         return atmsel
 
     def optimize_loop(self, atmsel, sched, actions):
RefactoringTool: No changes to modlib/modeller/automodel/parallel.py
RefactoringTool: No changes to modlib/modeller/automodel/randomize.py
RefactoringTool: No changes to modlib/modeller/automodel/refine.py
RefactoringTool: No changes to modlib/modeller/library_restraints/angles.py
RefactoringTool: No changes to modlib/modeller/library_restraints/bonds.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi1.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi2.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi3.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi4.py
RefactoringTool: No changes to modlib/modeller/library_restraints/impropers.py
RefactoringTool: No changes to modlib/modeller/library_restraints/omega_dihedrals.py
RefactoringTool: No changes to modlib/modeller/library_restraints/phi_psi.py
RefactoringTool: No changes to modlib/modeller/mmcif/data.py
RefactoringTool: Refactored modlib/modeller/mmcif/writer.py
--- modlib/modeller/mmcif/writer.py	(original)
+++ modlib/modeller/mmcif/writer.py	(refactored)
@@ -4,7 +4,7 @@
 # which works as far back as 2.3, so imports need to be protected by a
 # version check
 
-from __future__ import print_function
+
 import sys
 import textwrap
 
@@ -12,7 +12,7 @@
 if sys.version_info[0] >= 3:
     _long_type = int
 else:
-    _long_type = long
+    _long_type = int
 
 class _LineWriter(object):
     def __init__(self, writer, line_len=80):
RefactoringTool: No changes to modlib/modeller/optimizers/actions.py
RefactoringTool: Refactored modlib/modeller/optimizers/builtin_optimizer.py
--- modlib/modeller/optimizers/builtin_optimizer.py	(original)
+++ modlib/modeller/optimizers/builtin_optimizer.py	(refactored)
@@ -9,7 +9,7 @@
         # delete the key entirely, as __getstate__ must return a non-empty
         # dict in order for our __setstate__ method to be called).
         d = self.__dict__.copy()
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             if key.endswith("_modpt") or key.endswith("__optpt"):
                 d[key] = None
         return d
@@ -21,7 +21,7 @@
         vars = params.copy()
         self._update_params(vars, ok_keys, extravars)
         for key in ok_keys:
-            if key not in vars.keys() \
+            if key not in list(vars.keys()) \
                and key not in ("edat", "libs", "actions", "schedule_scale"):
                 raise ValueError("a value must be given for %s" % key)
 
RefactoringTool: No changes to modlib/modeller/optimizers/conjugate_gradients.py
RefactoringTool: No changes to modlib/modeller/optimizers/molecular_dynamics.py
RefactoringTool: Refactored modlib/modeller/optimizers/optimizer.py
--- modlib/modeller/optimizers/optimizer.py	(original)
+++ modlib/modeller/optimizers/optimizer.py	(refactored)
@@ -10,7 +10,7 @@
         return self.atmsel
 
     def _update_params(self, params, ok_keys, vars):
-        for key in vars.keys():
+        for key in list(vars.keys()):
             if key in ok_keys:
                 params[key] = vars[key]
             else:
RefactoringTool: No changes to modlib/modeller/optimizers/quasi_newton.py
RefactoringTool: No changes to modlib/modeller/optimizers/state_optimizer.py
RefactoringTool: No changes to modlib/modeller/parallel/communicator.py
RefactoringTool: Refactored modlib/modeller/parallel/data_types.py
--- modlib/modeller/parallel/data_types.py	(original)
+++ modlib/modeller/parallel/data_types.py	(refactored)
@@ -3,7 +3,7 @@
 import sys
 
 try:
-    import cPickle as pickle
+    import pickle as pickle
 except ImportError:
     import pickle
 
RefactoringTool: Refactored modlib/modeller/parallel/job.py
--- modlib/modeller/parallel/job.py	(original)
+++ modlib/modeller/parallel/job.py	(refactored)
@@ -106,7 +106,7 @@
         if id and id in pending_slaves:
             slave = pending_slaves.pop(id)
             connected_slaves[id] = slave
-            print("Identified slave %s " % str(slave))
+            print(("Identified slave %s " % str(slave)))
             slave.accept_connection(sock)
             slave.set_directory(self.cwd)
             if sys.path[0] != '':
@@ -117,7 +117,7 @@
             return slave
         elif id and id in connected_slaves:
             slave = connected_slaves[id]
-            print("Reconnect from slave %s " % str(slave))
+            print(("Reconnect from slave %s " % str(slave)))
             slave.accept_connection(sock)
         else:
             print("Ignoring request from unknown slave")
@@ -159,7 +159,7 @@
         """Run all tasks and return all the results, in the same order that they
            were submitted, when all the jobs have completed."""
         tasks = self.tasks[:]
-        print("Running %d tasks on %d slaves" % (len(tasks), len(self)))
+        print(("Running %d tasks on %d slaves" % (len(tasks), len(self))))
         self.push_tasks_to_slaves()
         while True:
             try:
@@ -174,7 +174,7 @@
     def yield_tasks_unordered(self):
         """Run all tasks and return their results (as a generator), in
            whatever order they complete."""
-        print("Running %d tasks on %d slaves" % (len(self.tasks), len(self)))
+        print(("Running %d tasks on %d slaves" % (len(self.tasks), len(self))))
         self.push_tasks_to_slaves()
         while True:
             try:
@@ -215,7 +215,7 @@
                 task = obj.task_results()
                 if task:
                     # The slave completed its task
-                    print("%s on %s completed" % (str(task), str(obj)))
+                    print(("%s on %s completed" % (str(task), str(obj))))
                     if len(self.tasks) > 0:
                         obj.run_task(self.tasks.pop(0))
                     return task
@@ -225,14 +225,14 @@
             except (NetworkError, TaskSetupError):
                 self.kill_slaves((obj,), sys.exc_info()[1])
         else:
-            print("Warning: slave %s reports data, but is not running a task" \
-                  % str(obj))
+            print(("Warning: slave %s reports data, but is not running a task" \
+                  % str(obj)))
 
     def kill_slaves(self, slaves, err=""):
         if err != "":
             err = "(%s) " % err
         for s in slaves:
-            print("%s failed %s- removing from %s" % (s, err, self))
+            print(("%s failed %s- removing from %s" % (s, err, self)))
             task = s.kill()
             if task:
                 self.tasks.append(task)
@@ -248,8 +248,8 @@
         timedout = [a for a in self if a.running_task() and \
                                     a.contact_timeout(self.heartbeat_timeout)]
         if len(timedout) > 0:
-            print("Did not hear from slaves %s in %d seconds" % \
-                  (str(timedout), self.heartbeat_timeout))
+            print(("Did not hear from slaves %s in %d seconds" % \
+                  (str(timedout), self.heartbeat_timeout)))
             self.kill_slaves(timedout)
 
     def push_tasks_to_slaves(self):
@@ -264,8 +264,8 @@
                 slave.run_task(t)
             # If a network error occurred, kill the slave and requeue the task
             except socket.error:
-                print("slave %s failed on run task with %s; removing from job" \
-                      % (slave, sys.exc_info()[1]))
+                print(("slave %s failed on run task with %s; removing from job" \
+                      % (slave, sys.exc_info()[1])))
                 slave.kill()
                 self.tasks.insert(0, t)
         self.expand_for_tasks()
RefactoringTool: No changes to modlib/modeller/parallel/local_slave.py
RefactoringTool: No changes to modlib/modeller/parallel/mypopen4.py
RefactoringTool: Refactored modlib/modeller/parallel/myspawn.py
--- modlib/modeller/parallel/myspawn.py	(original)
+++ modlib/modeller/parallel/myspawn.py	(refactored)
@@ -10,7 +10,7 @@
        ``output``."""
 
     fp = open(output, "w")
-    print("%s >& %s" % (cmd, output))
+    print(("%s >& %s" % (cmd, output)))
     if sys.platform == 'win32':
         _myspawn_win32(cmd, fp)
     else:
@@ -27,4 +27,4 @@
     # Ignore Windows "file not found" errors, so that behavior is consistent
     # between Unix and Windows
     except WindowsError:
-        print("WindowsError: %s (ignored)" % sys.exc_info()[1])
+        print(("WindowsError: %s (ignored)" % sys.exc_info()[1]))
RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_job.py
RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_slave.py
RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_array.py
--- modlib/modeller/parallel/sge_qsub_array.py	(original)
+++ modlib/modeller/parallel/sge_qsub_array.py	(refactored)
@@ -36,7 +36,7 @@
         outlines = output.readlines()
         output.close()
         for line in outlines:
-            print(line.rstrip('\r\n'))
+            print((line.rstrip('\r\n')))
         a.require_clean_exit()
         self._set_jobid(outlines)
 
RefactoringTool: No changes to modlib/modeller/parallel/sge_qsub_job.py
RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_slave.py
--- modlib/modeller/parallel/sge_qsub_slave.py	(original)
+++ modlib/modeller/parallel/sge_qsub_slave.py	(refactored)
@@ -38,7 +38,7 @@
         qsub = "qsub -S /bin/sh -o '%s' -N '%s' %s %s" % \
               (output, name, self.standard_options, self._options)
         cmd = "%s -slave %s" % (path, id)
-        print("%s | %s" % (cmd, qsub))
+        print(("%s | %s" % (cmd, qsub)))
         a = MyPopen4(qsub)
         (input, output) = (a.stdin, a.stdout)
         input.write(cmd + '\n')
@@ -46,7 +46,7 @@
         outlines = output.readlines()
         output.close()
         for line in outlines:
-            print(line.rstrip('\r\n'))
+            print((line.rstrip('\r\n')))
         a.require_clean_exit()
         self._set_jobid(outlines)
 
RefactoringTool: No changes to modlib/modeller/parallel/slave.py
RefactoringTool: No changes to modlib/modeller/parallel/slave_communicator.py
RefactoringTool: Refactored modlib/modeller/parallel/slaveloop.py
--- modlib/modeller/parallel/slaveloop.py	(original)
+++ modlib/modeller/parallel/slaveloop.py	(refactored)
@@ -51,14 +51,14 @@
                         master.send_data(communicator.ErrorWrapper(detail))
                     except socket.error:
                         detail2 = sys.exc_info()[1]
-                        print("Warning: ignored exception " + str(detail2) \
+                        print(("Warning: ignored exception " + str(detail2) \
                               + " when trying to send error state " \
-                              + str(detail) + " back to master")
+                              + str(detail) + " back to master"))
                         raise detail
                 raise
 
     def run(self):
-        print("Slave startup: connect to master at %s" % self.addr)
+        print(("Slave startup: connect to master at %s" % self.addr))
         (host, port, identifier) = self.addr.split(":", 2)
         port = int(port)
         lock = threading.Lock()
RefactoringTool: No changes to modlib/modeller/parallel/slavestate.py
RefactoringTool: No changes to modlib/modeller/parallel/ssh_slave.py
RefactoringTool: No changes to modlib/modeller/parallel/task.py
RefactoringTool: No changes to modlib/modeller/scripts/align_strs_seq.py
RefactoringTool: No changes to modlib/modeller/scripts/asgl_principal_components.py
RefactoringTool: No changes to modlib/modeller/scripts/cispeptide.py
RefactoringTool: No changes to modlib/modeller/scripts/complete_pdb.py
RefactoringTool: No changes to modlib/modeller/scripts/fit.py
RefactoringTool: No changes to modlib/modeller/scripts/principal_components.py
RefactoringTool: No changes to modlib/modeller/scripts/sequence_srch.py
RefactoringTool: Refactored modlib/modeller/top_interpreter/__init__.py
--- modlib/modeller/top_interpreter/__init__.py	(original)
+++ modlib/modeller/top_interpreter/__init__.py	(refactored)
@@ -65,7 +65,7 @@
             if len(line) > 0:
                 try:
                     self._parse_top_ini_line(line.split(None, 4), vars)
-                except TypeError, detail:
+                except TypeError as detail:
                     mod_log_write("read_top__E> " + str(detail))
                     mod_log_write("             top.ini line: " + line)
                     raise
@@ -113,7 +113,7 @@
                 self._set_top_vars(vars)
                 try:
                     fh = self._open_include_file(self.variables['include_file'])
-                except IOError, detail:
+                except IOError as detail:
                     mod_log_write("runlines__E> " + str(detail))
                     mod_log_write("             TOP Command line: " + line)
                     raise
@@ -160,7 +160,7 @@
                     indxca = self._run_top_cmd(cmd, indxca, lines, callstack,
                                                subrout)
                     _modeller.mod_top_post()
-            except (IndexError, SyntaxError, TypeError), detail:
+            except (IndexError, SyntaxError, TypeError) as detail:
                 mod_log_write("runlines__E> " + str(detail))
                 mod_log_write("             TOP Command line: " + line)
                 raise
RefactoringTool: No changes to modlib/modeller/top_interpreter/commands.py
RefactoringTool: Refactored modlib/modeller/top_interpreter/topcmds.py
--- modlib/modeller/top_interpreter/topcmds.py	(original)
+++ modlib/modeller/top_interpreter/topcmds.py	(refactored)
@@ -19,7 +19,7 @@
         if not isinstance(vars, (list, tuple)):
             vars = (vars,)
         for var in vars:
-            if keys.has_key(var):
+            if var in keys:
                 args.append(keys[var])
             else:
                 args.append(self.vars[var])
RefactoringTool: Refactored modlib/modeller/top_interpreter/util.py
--- modlib/modeller/top_interpreter/util.py	(original)
+++ modlib/modeller/top_interpreter/util.py	(refactored)
@@ -1,7 +1,7 @@
 import _modeller
 
 def set_topvars(topvardict, vars, topini):
-    for name in topvardict.keys():
+    for name in list(topvardict.keys()):
         value = topvardict[name]
         if value is None:
             continue
RefactoringTool: Refactored modlib/modeller/top_interpreter/variables.py
--- modlib/modeller/top_interpreter/variables.py	(original)
+++ modlib/modeller/top_interpreter/variables.py	(refactored)
@@ -32,11 +32,11 @@
     def __init__(self, topcmds):
         self._topcmds = topcmds
         self._topvars = {}
-        for var in self._deftops.keys():
+        for var in list(self._deftops.keys()):
             self._ourvars[var] = self._deftops[var]
-        for var in self._edat_members.keys():
+        for var in list(self._edat_members.keys()):
             self._ourvars[var] = self._edat_members[var]
-        for var in self._io_members.keys():
+        for var in list(self._io_members.keys()):
             self._ourvars[var] = self._io_members[var]
 
     def __setitem__(self, key, value):
RefactoringTool: No changes to modlib/modeller/util/array.py
RefactoringTool: No changes to modlib/modeller/util/logger.py
RefactoringTool: No changes to modlib/modeller/util/matrix.py
RefactoringTool: No changes to modlib/modeller/util/modlist.py
RefactoringTool: Refactored modlib/modeller/util/modobject.py
--- modlib/modeller/util/modobject.py	(original)
+++ modlib/modeller/util/modobject.py	(refactored)
@@ -1,8 +1,8 @@
 class modobject(object):
     def __setattr__(self, name, val):
         if name not in dir(self):
-            print("runcmd_____W>: creation of new member '%s' in %s: "
-                  "possible typo!" % (name, str(self)))
+            print(("runcmd_____W>: creation of new member '%s' in %s: "
+                  "possible typo!" % (name, str(self))))
         object.__setattr__(self, name, val)
 
     def __getstate__(self):
@@ -11,7 +11,7 @@
         # delete the key entirely, as __getstate__ must return a non-empty
         # dict in order for our __setstate__ method to be called).
         d = self.__dict__.copy()
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             if key.endswith("_modpt"):
                 d[key] = None
         return d
RefactoringTool: Refactored modlib/modeller/util/modutil.py
--- modlib/modeller/util/modutil.py	(original)
+++ modlib/modeller/util/modutil.py	(refactored)
@@ -17,7 +17,7 @@
         else:
             return indx
     elif isinstance(indx, slice):
-        return range(*indx.indices(len(seqtype)))
+        return list(range(*indx.indices(len(seqtype))))
     elif lookup_func is not None:
         args = lookup_args + (indx,)
         int_indx = lookup_func(*args)
RefactoringTool: Files that were modified:
RefactoringTool: modlib/modeller/__init__.py
RefactoringTool: modlib/modeller/alignment.py
RefactoringTool: modlib/modeller/alnsequence.py
RefactoringTool: modlib/modeller/alnstructure.py
RefactoringTool: modlib/modeller/atom_type.py
RefactoringTool: modlib/modeller/coordinates.py
RefactoringTool: modlib/modeller/density.py
RefactoringTool: modlib/modeller/energy_data.py
RefactoringTool: modlib/modeller/energy_profile.py
RefactoringTool: modlib/modeller/environ.py
RefactoringTool: modlib/modeller/excluded_pair.py
RefactoringTool: modlib/modeller/excluded_pair_list.py
RefactoringTool: modlib/modeller/features.py
RefactoringTool: modlib/modeller/forms.py
RefactoringTool: modlib/modeller/gbsa.py
RefactoringTool: modlib/modeller/group_restraints.py
RefactoringTool: modlib/modeller/id_table.py
RefactoringTool: modlib/modeller/information.py
RefactoringTool: modlib/modeller/io_data.py
RefactoringTool: modlib/modeller/libraries.py
RefactoringTool: modlib/modeller/model.py
RefactoringTool: modlib/modeller/model_topology.py
RefactoringTool: modlib/modeller/modfile.py
RefactoringTool: modlib/modeller/normalized_dope.py
RefactoringTool: modlib/modeller/orient.py
RefactoringTool: modlib/modeller/parameters.py
RefactoringTool: modlib/modeller/physical.py
RefactoringTool: modlib/modeller/profile.py
RefactoringTool: modlib/modeller/pseudo_atom.py
RefactoringTool: modlib/modeller/pseudo_atom_list.py
RefactoringTool: modlib/modeller/pssmdb.py
RefactoringTool: modlib/modeller/residue.py
RefactoringTool: modlib/modeller/restraints.py
RefactoringTool: modlib/modeller/rigid_body.py
RefactoringTool: modlib/modeller/rigid_body_list.py
RefactoringTool: modlib/modeller/salign.py
RefactoringTool: modlib/modeller/saxsdata.py
RefactoringTool: modlib/modeller/schedule.py
RefactoringTool: modlib/modeller/secondary_structure.py
RefactoringTool: modlib/modeller/selection.py
RefactoringTool: modlib/modeller/sequence.py
RefactoringTool: modlib/modeller/sequence_db.py
RefactoringTool: modlib/modeller/soap_loop.py
RefactoringTool: modlib/modeller/soap_peptide.py
RefactoringTool: modlib/modeller/soap_pp.py
RefactoringTool: modlib/modeller/soap_protein_od.py
RefactoringTool: modlib/modeller/superpose.py
RefactoringTool: modlib/modeller/symmetry.py
RefactoringTool: modlib/modeller/symmetry_list.py
RefactoringTool: modlib/modeller/terms.py
RefactoringTool: modlib/modeller/test.py
RefactoringTool: modlib/modeller/topology.py
RefactoringTool: modlib/modeller/virtual_atom.py
RefactoringTool: modlib/modeller/automodel/__init__.py
RefactoringTool: modlib/modeller/automodel/allhmodel.py
RefactoringTool: modlib/modeller/automodel/assess.py
RefactoringTool: modlib/modeller/automodel/automodel.py
RefactoringTool: modlib/modeller/automodel/autosched.py
RefactoringTool: modlib/modeller/automodel/dope_loopmodel.py
RefactoringTool: modlib/modeller/automodel/dopehr_loopmodel.py
RefactoringTool: modlib/modeller/automodel/generate.py
RefactoringTool: modlib/modeller/automodel/loopmodel.py
RefactoringTool: modlib/modeller/automodel/parallel.py
RefactoringTool: modlib/modeller/automodel/randomize.py
RefactoringTool: modlib/modeller/automodel/refine.py
RefactoringTool: modlib/modeller/library_restraints/angles.py
RefactoringTool: modlib/modeller/library_restraints/bonds.py
RefactoringTool: modlib/modeller/library_restraints/chi1.py
RefactoringTool: modlib/modeller/library_restraints/chi2.py
RefactoringTool: modlib/modeller/library_restraints/chi3.py
RefactoringTool: modlib/modeller/library_restraints/chi4.py
RefactoringTool: modlib/modeller/library_restraints/impropers.py
RefactoringTool: modlib/modeller/library_restraints/omega_dihedrals.py
RefactoringTool: modlib/modeller/library_restraints/phi_psi.py
RefactoringTool: modlib/modeller/mmcif/data.py
RefactoringTool: modlib/modeller/mmcif/writer.py
RefactoringTool: modlib/modeller/optimizers/actions.py
RefactoringTool: modlib/modeller/optimizers/builtin_optimizer.py
RefactoringTool: modlib/modeller/optimizers/conjugate_gradients.py
RefactoringTool: modlib/modeller/optimizers/molecular_dynamics.py
RefactoringTool: modlib/modeller/optimizers/optimizer.py
RefactoringTool: modlib/modeller/optimizers/quasi_newton.py
RefactoringTool: modlib/modeller/optimizers/state_optimizer.py
RefactoringTool: modlib/modeller/parallel/communicator.py
RefactoringTool: modlib/modeller/parallel/data_types.py
RefactoringTool: modlib/modeller/parallel/job.py
RefactoringTool: modlib/modeller/parallel/local_slave.py
RefactoringTool: modlib/modeller/parallel/mypopen4.py
RefactoringTool: modlib/modeller/parallel/myspawn.py
RefactoringTool: modlib/modeller/parallel/sge_pe_job.py
RefactoringTool: modlib/modeller/parallel/sge_pe_slave.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_array.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_job.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_slave.py
RefactoringTool: modlib/modeller/parallel/slave.py
RefactoringTool: modlib/modeller/parallel/slave_communicator.py
RefactoringTool: modlib/modeller/parallel/slaveloop.py
RefactoringTool: modlib/modeller/parallel/slavestate.py
RefactoringTool: modlib/modeller/parallel/ssh_slave.py
RefactoringTool: modlib/modeller/parallel/task.py
RefactoringTool: modlib/modeller/scripts/align_strs_seq.py
RefactoringTool: modlib/modeller/scripts/asgl_principal_components.py
RefactoringTool: modlib/modeller/scripts/cispeptide.py
RefactoringTool: modlib/modeller/scripts/complete_pdb.py
RefactoringTool: modlib/modeller/scripts/fit.py
RefactoringTool: modlib/modeller/scripts/principal_components.py
RefactoringTool: modlib/modeller/scripts/sequence_srch.py
RefactoringTool: modlib/modeller/top_interpreter/__init__.py
RefactoringTool: modlib/modeller/top_interpreter/commands.py
RefactoringTool: modlib/modeller/top_interpreter/topcmds.py
RefactoringTool: modlib/modeller/top_interpreter/util.py
RefactoringTool: modlib/modeller/top_interpreter/variables.py
RefactoringTool: modlib/modeller/util/array.py
RefactoringTool: modlib/modeller/util/logger.py
RefactoringTool: modlib/modeller/util/matrix.py
RefactoringTool: modlib/modeller/util/modlist.py
RefactoringTool: modlib/modeller/util/modobject.py
RefactoringTool: modlib/modeller/util/modutil.py
 * Non-PEP517 builds are deprecated for ebuilds using plain distutils.
 * Please migrate to DISTUTILS_USE_PEP517=setuptools.
 * Please see Python Guide for more details:
 *   https://projects.gentoo.org/python/guide/distutils.html
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
 * python3_10: running distutils-r1_run_phase python_compile
python3.10 setup.py build -j 32
/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils.core import setup, Extension
running build
running build_ext
building '_modeller' extension
creating /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_10/temp.linux-x86_64-3.10
x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I../include -I../include/x86_64-intel8 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/python3.10 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_10/temp.linux-x86_64-3.10/modeller_wrap.o
modeller_wrap.c: In function ‘python_cb_fangle’:
modeller_wrap.c:3688:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3688 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
In file included from /usr/include/python3.10/Python.h:130,
                 from modeller_wrap.c:194:
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_feval’:
modeller_wrap.c:3717:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3717 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_fderiv’:
modeller_wrap.c:3747:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3747 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_teval’:
modeller_wrap.c:3791:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3791 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_simloc’:
modeller_wrap.c:3849:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3849 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_reval’:
modeller_wrap.c:3887:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3887 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_range’:
modeller_wrap.c:3936:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3936 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_violation’:
modeller_wrap.c:3985:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 3985 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_mean’:
modeller_wrap.c:4021:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 4021 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_action’:
modeller_wrap.c:4041:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 4041 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘python_cb_log’:
modeller_wrap.c:4065:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
 4065 |   result = PyEval_CallObject(func, arglist);
      |   ^~~~~~
/usr/include/python3.10/ceval.h:17:43: note: declared here
   17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modeller_wrap.c: In function ‘pyfile_strreadlinefunc’:
modeller_wrap.c:4782:18: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 4782 |     char *utf8 = PyUnicode_AsUTF8(result);
      |                  ^~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_10/temp.linux-x86_64-3.10/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib64 -lmodeller -lglib-2.0 -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_10/lib/_modeller.cpython-310-x86_64-linux-gnu.so
>>> Source compiled.
>>> Test phase [not enabled]: sci-chemistry/modeller-9.25

>>> Install sci-chemistry/modeller-9.25 into /var/tmp/portage/sci-chemistry/modeller-9.25/image
 * python3_10: running distutils-r1_run_phase python_install
python3.10 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10
/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils.core import setup, Extension
running install
running install_lib
creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10
creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr
creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr/lib
creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr/lib/python3.10
creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr/lib/python3.10/site-packages
copying /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_10/lib/_modeller.cpython-310-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr/lib/python3.10/site-packages
running install_egg_info
Writing /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.10/usr/lib/python3.10/site-packages/Modeller-0.0.0-py3.10.egg-info
 * Python extension modules (*.so) found installed. Please set:
 *   DISTUTILS_EXT=1
 * in the ebuild.
 * Using python3.10 in global scope
 * python3_10: running distutils-r1_run_phase python_install_all
 * python_foreach_impl has been called directly while using distutils-r1.
 * Please redefine python_*() phase functions to meet your expectations
 * instead.
 * python3_10: running python_domodule modlib/modeller
 * Optimize Python modules for //usr/lib/python3.10/site-packages/
 * python3_10: running python_doscript bin/modslave.py
>>> Completed installing sci-chemistry/modeller-9.25 into /var/tmp/portage/sci-chemistry/modeller-9.25/image

 * Final size of build directory: 148456 KiB (144.9 MiB)
 * Final size of installed tree:   57404 KiB ( 56.0 MiB)

 * Verifying compiled files for python3.10
 * 
 * QA Notice: The following deprecated .egg or .egg-info files were found.
 * Please migrate the ebuild to use the PEP517 build.
 * 
 *   /usr/lib/python3.10/site-packages/Modeller-0.0.0-py3.10.egg-info
strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version
   /opt/modeller/bin/mod9.25_x86_64-intel8
   /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.100
   /usr/lib/python3.10/site-packages/_modeller.cpython-310-x86_64-linux-gnu.so
   /opt/modeller/lib/x86_64-intel8/libintlc.so.5
   /opt/modeller/lib/x86_64-intel8/libifcore.so.5
   /opt/modeller/lib/x86_64-intel8/libsaxs.so
   /opt/modeller/lib/x86_64-intel8/libsvml.so
   /opt/modeller/lib/x86_64-intel8/libpython2.3.so.1.0
   /opt/modeller/lib/x86_64-intel8/libimf.so
   /opt/modeller/lib/x86_64-intel8/libhdf5.so.103
   /opt/modeller/lib/x86_64-intel8/libmodeller.so.12
>>> Done.
 * Obtain a license Key from
 * http://salilab.org/modeller/registration.html
 * And run this before using modeller:
 * emerge --config =sci-chemistry/modeller-9.25
 * That way you can [re]enter your license key.