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Gentoo's Bugzilla – Attachment 764375 Details for
Bug 832745
sci-chemistry/modeller-10.5 installs files with unresolved SONAME dependencies
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build.log
build.log (text/plain), 89.04 KB, created by
Agostino Sarubbo
on 2022-02-05 08:03:08 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2022-02-05 08:03:08 UTC
Size:
89.04 KB
patch
obsolete
> * Package: sci-chemistry/modeller-9.25 > * Repository: gentoo > * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_musl kernel_linux python_targets_python3_8 python_targets_python3_9 userland_GNU > * 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/d43e44fd025825ec24fe5791ac96f5692143b27b (Fri Feb 4 09:37:03 UTC 2022) >@@@@@ END @@@@@ > > > >################## ># emerge --info: # >################## >!!! It seems /run is not mounted. Process management may malfunction. >Portage 3.0.30 (python 3.10.2-final-0, default/linux/amd64/17.0/musl/hardened, gcc-11.2.1, musl-1.2.2-r7, 4.19.174-gentoo x86_64) >================================================================= >System uname: Linux-4.19.174-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-libc >KiB Mem: 264046488 total, 61637124 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Fri, 04 Feb 2022 09:37:00 +0000 >sh bash 5.1_p16 >ld GNU ld (Gentoo 2.37_p1 p2) 2.37 >app-misc/pax-utils: 1.3.3::gentoo >app-shells/bash: 5.1_p16::gentoo >dev-lang/perl: 5.34.0-r6::gentoo >dev-lang/python: 3.8.12_p1-r2::gentoo, 3.9.10-r1::gentoo, 3.10.2-r1::gentoo >dev-util/cmake: 3.22.2::gentoo >dev-util/meson: 0.60.3::gentoo >sys-apps/baselayout: 2.8::gentoo >sys-apps/openrc: 0.44.10::gentoo >sys-apps/sandbox: 2.29::gentoo >sys-devel/autoconf: 2.71-r1::gentoo >sys-devel/automake: 1.16.5::gentoo >sys-devel/binutils: 2.37_p1-r2::gentoo >sys-devel/binutils-config: 5.4::gentoo >sys-devel/gcc: 11.2.1_p20220115::gentoo >sys-devel/gcc-config: 2.5-r1::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.16::gentoo (virtual/os-headers) >sys-libs/musl: 1.2.2-r7::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-max-age: 24 > sync-rsync-verify-jobs: 1 > sync-rsync-extra-opts: > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* modeller" >CBUILD="x86_64-gentoo-linux-musl" >CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" >CHOST="x86_64-gentoo-linux-musl" >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 -pipe -march=x86-64 -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" >ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY 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" >FCFLAGS="-O2 -pipe -march=x86-64 -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 network-sandbox news parallel-fetch pid-sandbox 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 -pipe -march=x86-64 -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" >INSTALL_MASK="charset.alias /usr/share/locale/locale.alias" >LANG="C.UTF8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j16" >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 crypt elogind hardened iconv ipv6 jumbo-build libglvnd libtirpc native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" PYTHON_TARGETS="python3_8 python3_9" USERLAND="GNU" >Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS > > > > > >############################## ># emerge history (qlop -mv): # >############################## >2022-02-04T10:50:32 >>> dev-lang/swig-4.0.2 > > > > >####################################### ># installed packages (qlist -ICvUSS): # >####################################### >acct-group/audio-0-r1:0 >acct-group/cdrom-0-r1:0 >acct-group/dialout-0-r1:0 >acct-group/disk-0-r1:0 >acct-group/input-0-r1:0 >acct-group/kmem-0-r1:0 >acct-group/kvm-0-r1:0 >acct-group/lp-0-r1:0 >acct-group/man-0-r1:0 >acct-group/messagebus-0-r1:0 >acct-group/portage-0:0 >acct-group/render-0-r1:0 >acct-group/sgx-0:0 >acct-group/sshd-0-r1:0 >acct-group/tape-0-r1:0 >acct-group/tty-0-r1:0 >acct-group/video-0-r1:0 >acct-user/man-1-r1:0 >acct-user/messagebus-0-r1:0 >acct-user/portage-0:0 >acct-user/sshd-0-r1:0 >app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax >app-admin/perl-cleaner-2.30:0 >app-arch/bzip2-1.0.8-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 split-usr -static -static-libs >app-arch/gzip-1.11:0 -pic -static >app-arch/libarchive-3.5.2:0/13 -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 xattr zlib -zstd >app-arch/tar-1.34:0 acl -minimal nls -selinux xattr >app-arch/unzip-6.0_p26:0 bzip2 -natspec unicode >app-arch/xz-utils-5.2.5-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 extra-filters nls split-usr -static-libs >app-arch/zstd-1.5.2:0/1 -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 -static-libs threads >app-crypt/gnupg-2.3.4:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -usb -user-socket -wks-server >app-crypt/gpgme-1.16.0:1/11 -common-lisp cxx -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs >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-1.0.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 >app-crypt/pinentry-1.2.0:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5 >app-crypt/rhash-1.4.2:0 -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 ssl -static-libs >app-editors/nano-6.0:0 -debug -justify -magic -minimal ncurses nls spell split-usr -static unicode >app-eselect/eselect-fontconfig-1.1-r1:0 >app-eselect/eselect-iptables-20211203:0 >app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0 >app-eselect/eselect-pinentry-0.7.2:0 >app-misc/c_rehash-1.7-r1:0 >app-misc/ca-certificates-20211016.3.72:0 -cacert >app-misc/editor-wrapper-4-r1:0 >app-misc/mime-types-2.1.53:0 -nginx >app-misc/pax-utils-1.3.3:0 -caps -debug -python -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 seccomp >app-misc/tmux-3.2a:0 -debug -selinux -utempter -vim-syntax >app-portage/eix-0.36.1:0 -debug -doc nls -sqlite >app-portage/elt-patches-20211104:0 >app-portage/gemato-16.2:0 gpg -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -tools >app-portage/gentoolkit-0.5.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >app-portage/portage-utils-0.93.3:0 nls openmp qmanifest qtegrity -static >app-shells/bash-5.1_p16:0 -afs -bashlogger -examples -mem-scramble net nls -plugins readline >app-shells/push-3.4:0 >app-shells/quoter-4.2:0 >app-text/ansifilter-2.18:0 -qt5 >app-text/build-docbook-catalog-2.2:0 >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-stylesheets-1.79.1-r2:0 -ruby >app-text/manpager-1:0 >app-text/sgml-common-0.6.3-r7:0 >app-text/xmlto-0.0.28-r8:0 -latex -text >dev-db/sqlite-3.37.2:3 -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/perl-5.34.0-r6:0/5.34 -berkdb -debug -doc -gdbm ithreads -minimal >dev-lang/python-3.10.2-r1:3.10 -bluetooth -build -examples gdbm hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml >dev-lang/python-3.9.10-r1:3.9 -bluetooth -build -examples gdbm hardened -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml >dev-lang/python-3.8.12_p1-r2:3.8 -bluetooth -build -examples gdbm hardened ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml >dev-lang/python-exec-2.4.8:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-lang/python-exec-conf-2.4.6:2 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >dev-lang/swig-4.0.2:0 -ccache -doc pcre >dev-lang/tcl-8.6.12:0/8.6 -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/elfutils-0.186:0 -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 -lzma nls -static-libs -test -threads utils -valgrind -zstd >dev-libs/expat-2.4.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples -static-libs unicode >dev-libs/glib-2.70.3:2 -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 -fam -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr >dev-libs/gmp-6.2.1-r2:0/10.4 -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 cxx -doc -pic -static-libs >dev-libs/gobject-introspection-1.70.0:0 -doctool -gtk-doc -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -test >dev-libs/gobject-introspection-common-1.70.0:0 >dev-libs/isl-0.24-r2:0/23 -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-2.5.5:0 >dev-libs/libbsd-0.11.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs >dev-libs/libevent-2.1.12:0/2.1-7 -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 threads -verbose-debug >dev-libs/libffi-3.4.2-r1:0/8 -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-1.9.4:0/20 -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 -o-flag-munging -static-libs >dev-libs/libgpg-error-1.44:0 -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 >dev-libs/libksba-1.6.0:0 -static-libs >dev-libs/libltdl-2.4.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs >dev-libs/libpcre-8.45:3 -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 cxx -jit -libedit pcre16 pcre32 readline recursion-limit split-usr -static-libs unicode zlib >dev-libs/libpcre2-10.39:0/3 -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 recursion-limit split-usr -static-libs unicode zlib >dev-libs/libpipeline-1.5.5:0 -test >dev-libs/libtasn1-4.18.0:0/6 -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 -valgrind >dev-libs/libunistring-0.9.10-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 -doc -static-libs >dev-libs/libuv-1.43.0:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 >dev-libs/libxml2-2.9.12-r5:2 -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 -icu ipv6 -lzma python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 readline -static-libs -test -verify-sig >dev-libs/libxslt-1.1.34-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 crypt -debug -examples -static-libs -verify-sig >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-1.2.1:0/3 -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-4.1.0_p13-r1:0/6 -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 >dev-libs/nettle-3.7.3:0/8-6 -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_neon cpu_flags_x86_aes -cpu_flags_x86_sha -doc gmp -static-libs -test >dev-libs/npth-1.6-r1:0 >dev-libs/openssl-1.1.1m:0/1.1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpu_flags_x86_sse2 -rfc3779 -sctp -sslv3 -static-libs -test -tls-compression -tls-heartbeat -vanilla >dev-libs/popt-1.18:0 -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/Devel-CheckLib-1.140.0:0 -test >dev-perl/Encode-Locale-1.50.0-r1:0 -test >dev-perl/File-Listing-6.140.0:0 -test >dev-perl/HTML-Parser-3.760.0:0 -test >dev-perl/HTML-Tagset-3.200.0-r2:0 >dev-perl/HTTP-Cookies-6.100.0:0 -test >dev-perl/HTTP-Date-6.50.0:0 >dev-perl/HTTP-Message-6.330.0:0 -test -test >dev-perl/HTTP-Negotiate-6.10.0-r2:0 -test >dev-perl/IO-HTML-1.4.0:0 -test >dev-perl/IO-Socket-INET6-2.720.0-r2:0 -test >dev-perl/IO-Socket-SSL-2.74.0:0 -examples -idn -test >dev-perl/libwww-perl-6.600.0-r1:0 ssl -test >dev-perl/Locale-gettext-1.70.0-r1:0 -test >dev-perl/LWP-MediaTypes-6.40.0:0 -test >dev-perl/LWP-Protocol-https-6.100.0:0 -test >dev-perl/Module-Build-0.423.100:0 -test >dev-perl/Mozilla-CA-20999999-r1:0 -test >dev-perl/Net-HTTP-6.210.0:0 -minimal -test >dev-perl/Net-SSLeay-1.900.0:0 -examples -examples -minimal -test >dev-perl/Socket6-0.290.0:0 -test >dev-perl/TimeDate-2.330.0-r1:0 -test >dev-perl/Try-Tiny-0.310.0:0 -minimal -test >dev-perl/URI-5.100.0:0 -test >dev-perl/WWW-RobotRules-6.20.0-r2:0 -test >dev-perl/XML-Parser-2.460.0-r2:0 >dev-python/appdirs-1.4.4-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >dev-python/certifi-3021.3.16-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/charset_normalizer-2.0.11:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/flit_core-3.6.0-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/idna-3.3:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >dev-python/importlib_resources-5.4.0-r3:0 -doc -python_targets_pypy3 python_targets_python3_8 -test >dev-python/installer-0.4.0_p20220124:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/jaraco-context-4.1.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/jaraco-functools-3.5.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/jaraco-text-3.7.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/jinja-3.0.3:0 -doc -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/markupsafe-2.0.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/more-itertools-8.12.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/ordered-set-4.1.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/packaging-21.3-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/pyparsing-3.0.7-r1:0 -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/pypax-0.9.5-r1:0 -ptpax python_targets_python3_8 python_targets_python3_9 xtpax >dev-python/PySocks-1.7.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >dev-python/requests-2.27.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -socks5 -test >dev-python/setuptools-60.7.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/setuptools_scm-6.4.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/tomli-2.0.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/urllib3-1.26.8:0 -brotli -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/wheel-0.37.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-python/zipp-3.7.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-util/cmake-3.22.2:0 -doc -emacs ncurses -qt5 -test -test >dev-util/desktop-file-utils-0.26-r1:0 -emacs >dev-util/glib-utils-2.70.3:0 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 >dev-util/gperf-3.1:0 >dev-util/gtk-doc-am-1.33.2:0 >dev-util/intltool-0.51.0-r2:0 >dev-util/meson-0.60.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test >dev-util/meson-format-array-0:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 >dev-util/ninja-1.10.2-r1:0 -doc -emacs -test -vim-syntax >dev-util/pkgconf-1.8.0-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 -test >dev-util/re2c-2.2:0 -debug -test >dev-vcs/git-2.35.1:0 blksha1 -cgi curl -cvs -doc -emacs -gnome-keyring gpg -highlight iconv -mediawiki -mediawiki-experimental nls pcre -perforce -perl -ppcsha1 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -subversion -test threads -tk webdav -xinetd >media-fonts/liberation-fonts-2.1.3:0 -X -X -fontforge >media-gfx/graphite2-1.3.14_p20210810-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 -perl -test >media-libs/fontconfig-2.13.1-r2:1.0 -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 -static-libs >media-libs/freetype-2.11.1:2 -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 -infinality png -static-libs -utils >media-libs/harfbuzz-3.3.1:0/3.0.0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cairo -debug -doc -experimental glib graphite -icu introspection -test truetype >media-libs/libpng-1.6.37-r2:0/16 -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 >net-dns/libidn2-2.3.2:0/2 -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 -verify-sig >net-firewall/iptables-1.8.7-r1:0/1.8.3 -conntrack ipv6 -netlink -nftables -pcap split-usr -static-libs >net-libs/gnutls-3.7.3:0/30 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -dane -doc -examples -guile idn nls openssl -pkcs11 seccomp -sslv2 -sslv3 -static-libs -test -test-full tls-heartbeat -tools -valgrind >net-libs/libmnl-1.0.4:0/0.2.0 -examples split-usr -static-libs >net-libs/nghttp2-1.46.0:0/1.14 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx -debug -hpack-tools -jemalloc -static-libs -test threads -utils -xml >net-misc/curl-7.81.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -adns -alt-svc -brotli -curl_ssl_gnutls -curl_ssl_mbedtls -curl_ssl_nss curl_ssl_openssl ftp -gnutls -gopher -hsts http2 -idn imap ipv6 -kerberos -ldap -mbedtls -nghttp3 -nss openssl pop3 progress-meter -quiche -rtmp -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -threads -zstd >net-misc/iputils-20210722-r1:0 arping -caps -clockdiff -doc filecaps -gcrypt -idn ipv6 -nettle nls -rarpd -rdisc ssl -static -test -tftpd -tracepath -traceroute6 >net-misc/netifrc-0.7.3:0 >net-misc/openssh-8.8_p1-r4:0 -X -X509 -abi_mips_n32 -audit -debug -hpn -kerberos -ldns -libedit -livecd pam pie scp -sctp -security-key -selinux ssl -static -test -xmss >net-misc/rsync-3.2.3-r5:0 acl -examples iconv ipv6 -lz4 ssl -stunnel -system-zlib xattr -xxhash -zstd >net-misc/wget-1.21.2:0 -cookie-check -debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid zlib >perl-core/CPAN-2.290.0-r1:0 >perl-core/Encode-3.120.0:0 >perl-core/File-Temp-0.231.100:0 >perl-core/Scalar-List-Utils-1.560.0:0 >sec-keys/openpgp-keys-gentoo-release-20220101:0 -test >sys-apps/acl-2.3.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls split-usr -static-libs >sys-apps/attr-2.5.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls split-usr -static-libs >sys-apps/baselayout-2.8:0 -build split-usr >sys-apps/coreutils-9.0-r1:0 acl -caps -gmp -hostname -kill -multicall nls -selinux split-usr -static -test -vanilla xattr >sys-apps/dbus-1.12.20-r4:0 -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 >sys-apps/debianutils-5.5:0 installkernel -static >sys-apps/diffutils-3.8:0 nls -static >sys-apps/elfix-0.9.5:0 -ptpax xtpax >sys-apps/file-5.41:0 -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 -lzma -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -seccomp -static-libs zlib >sys-apps/findutils-4.9.0:0 nls -selinux -static -test >sys-apps/gawk-5.1.1-r1:0 -mpfr nls readline >sys-apps/gentoo-functions-0.15:0 >sys-apps/grep-3.7:0 nls pcre -static >sys-apps/groff-1.22.4:0 -X -examples -uchardet >sys-apps/help2man-1.48.5:0 nls >sys-apps/install-xattr-0.8:0 >sys-apps/iproute2-5.16.0:0 -atm -berkdb -bpf -caps -elf iptables ipv6 -libbsd -minimal -selinux >sys-apps/kbd-2.4.0:0 nls pam -test >sys-apps/kmod-29:0 -debug -doc lzma -pkcs7 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs tools zlib -zstd >sys-apps/less-590:0 pcre unicode >sys-apps/man-db-2.9.4-r1:0 -berkdb -gdbm manpager -nls seccomp -selinux -static-libs zlib >sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static >sys-apps/openrc-0.44.10:0 -audit -bash -debug ncurses netifrc -newnet pam -selinux -sysv-utils unicode >sys-apps/portage-3.0.30-r1:0 -apidoc -build -doc -gentoo-dev ipc native-extensions -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 rsync-verify -selinux -test xattr >sys-apps/sandbox-2.29:0 -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-4.8:0 acl nls -selinux -static >sys-apps/shadow-4.11.1:0/4 acl -audit -bcrypt -cracklib nls pam -selinux -skey split-usr -su xattr >sys-apps/systemd-tmpfiles-249.9:0 -selinux -test >sys-apps/sysvinit-3.01:0 -ibm -selinux -static >sys-apps/texinfo-6.8:0 nls standalone -static >sys-apps/util-linux-2.37.3-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_8 python_targets_python3_9 readline -rtas -selinux -slang split-usr -static-libs su suid -systemd -test -tty-helpers -udev unicode >sys-apps/which-2.21:0 >sys-auth/elogind-246.10-r2:0 acl -audit cgroup-hybrid -debug -doc pam -policykit -selinux >sys-auth/pambase-20211218-r1:0 -caps -debug elogind -gnome-keyring -homed -minimal -mktemp nullok -pam_krb5 -pam_ssh passwdqc -pwhistory -pwquality -securetty -selinux sha512 -systemd -yescrypt >sys-auth/passwdqc-2.0.2-r1:0 >sys-devel/autoconf-2.71-r1:2.71 -emacs >sys-devel/autoconf-archive-2021.02.19-r1:0 >sys-devel/autoconf-wrapper-20220130:0 >sys-devel/automake-1.16.5:1.16 -test >sys-devel/automake-wrapper-11:0 >sys-devel/binutils-2.37_p1-r2:2.37 -cet -default-gold -doc gold -multitarget nls -pgo plugins -static-libs -test -vanilla >sys-devel/binutils-config-5.4:0 native-symlinks >sys-devel/bison-3.8.2:0 -examples nls -static -test >sys-devel/flex-2.6.4-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 -test >sys-devel/gcc-11.2.1_p20220115:11 -ada -cet -custom-cflags cxx -d -debug -doc -fixed-point -fortran -go graphite hardened -jit -libssp lto -multilib -nls nptl -objc -objc++ -objc-gc openmp -pch -pgo pie -sanitize ssp -systemtap -test -valgrind -vanilla -vtv -zstd >sys-devel/gcc-config-2.5-r1:0 cc-wrappers native-symlinks >sys-devel/gettext-0.21-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 acl -cvs cxx -doc -emacs -git -java -java ncurses -nls openmp -static-libs >sys-devel/gnuconfig-20210107:0 >sys-devel/libtool-2.4.6-r6:2 -vanilla >sys-devel/m4-1.4.19:0 -examples nls >sys-devel/make-4.3:0 -guile nls -static >sys-devel/patch-2.7.6-r4:0 -static -test xattr >sys-fs/e2fsprogs-1.46.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cron -fuse -lto -nls split-usr -static-libs threads tools >sys-fs/udev-249.9:0 -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 kmod -selinux split-usr -test >sys-fs/udev-init-scripts-35:0 >sys-kernel/installkernel-gentoo-4:0 -grub >sys-kernel/linux-headers-5.16:0 -headers-only >sys-libs/argp-standalone-1.4.1-r1:0 -static-libs >sys-libs/binutils-libs-2.37_p1-r2:0/2.37 -64-bit-bfd -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cet -multitarget nls -static-libs >sys-libs/fts-standalone-1.2.7:0 -static-libs >sys-libs/gdbm-1.22:0/6 -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 >sys-libs/libcap-2.63:0 -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-2.5.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs -test >sys-libs/musl-1.2.2-r7:0 -headers-only >sys-libs/ncurses-6.3_p20211106:0/6 -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 -static-libs -test tinfo -trace >sys-libs/obstack-standalone-1.1:0 -static-libs >sys-libs/pam-1.5.2-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 -berkdb -debug -filecaps -nis -selinux >sys-libs/readline-8.1_p2:0/8 -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 >sys-libs/zlib-1.2.11-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 minizip split-usr -static-libs >sys-process/procps-3.3.17-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 elogind kill -modern-top ncurses nls -selinux split-usr -static-libs -systemd -test unicode >sys-process/psmisc-23.4-r1:0 -X ipv6 nls -selinux >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/awk-1:0 >virtual/dev-manager-0-r2:0 >virtual/editor-0-r3:0 >virtual/libc-1-r1:0 >virtual/libcrypt-1-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 -static-libs >virtual/libelf-3:0/1 -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-232-r5:0/1 -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/os-headers-0-r2:0 >virtual/package-manager-1:0 >virtual/pager-0:0 >virtual/perl-Carp-1.520.0-r1:0 >virtual/perl-Compress-Raw-Bzip2-2.101.0:0 >virtual/perl-Compress-Raw-Zlib-2.101.0:0 >virtual/perl-CPAN-2.290.0:0 >virtual/perl-CPAN-Meta-2.150.10-r5:0 >virtual/perl-CPAN-Meta-Requirements-2.140.0-r7:0 >virtual/perl-CPAN-Meta-YAML-0.18.0-r7:0 >virtual/perl-Data-Dumper-2.179.0:0 >virtual/perl-Digest-MD5-2.580.0:0 >virtual/perl-Encode-3.120.0:0 >virtual/perl-Exporter-5.760.0:0 >virtual/perl-ExtUtils-CBuilder-0.280.236:0 >virtual/perl-ExtUtils-Install-2.200.0:0 >virtual/perl-ExtUtils-MakeMaker-7.620.0:0 >virtual/perl-ExtUtils-Manifest-1.730.0:0 >virtual/perl-ExtUtils-ParseXS-3.430.0:0 >virtual/perl-File-Spec-3.800.0:0 >virtual/perl-File-Temp-0.231.100:0 >virtual/perl-Getopt-Long-2.520.0:0 >virtual/perl-IO-1.460.0:0 >virtual/perl-IO-Compress-2.102.0:0 >virtual/perl-IO-Socket-IP-0.410.0:0 >virtual/perl-JSON-PP-4.60.0:0 >virtual/perl-libnet-3.130.0:0 ssl >virtual/perl-MIME-Base64-3.160.0:0 >virtual/perl-Module-Metadata-1.0.37-r1:0 >virtual/perl-parent-0.238.0-r1:0 >virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0 >virtual/perl-Perl-OSType-1.10.0-r5:0 >virtual/perl-podlators-4.140.0-r2:0 >virtual/perl-Scalar-List-Utils-1.560.0:0 >virtual/perl-Test-Harness-3.430.0:0 >virtual/perl-Text-ParseWords-3.300.0-r8:0 >virtual/perl-Time-Local-1.300.0:0 >virtual/perl-version-0.992.800:0 >virtual/perl-XSLoader-0.300.0-r4:0 >virtual/pkgconfig-2-r1:0 >virtual/service-manager-1:0 >virtual/ssh-0:0 -minimal >virtual/tmpfiles-0-r1:0 >virtual/ttf-fonts-1-r1:0 >virtual/udev-217-r3:0 >virtual/yacc-0:0 >www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9 >x11-libs/cairo-1.16.0-r5:0 -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 -gles2-only glib -opengl -static-libs svg -utils -valgrind >x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -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 >x11-misc/shared-mime-info-2.1:0 > > >####################### ># 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 ... >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 >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... >/var/tmp/portage/sci-chemistry/modeller-9.25/temp/environment: line 2726: type: locale: not found >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... > * python3_8: running distutils-r1_run_phase python_compile >python3.8 setup.py build -j 16 >running build >running build_ext >building '_modeller' extension >creating /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8 >x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -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/lib/glib-2.0/include -I/usr/include/python3.8 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8/modeller_wrap.o >modeller_wrap.c: In function 'pyfile_strreadlinefunc': >modeller_wrap.c:4319:18: warning: initialization discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] > 4319 | char *utf8 = PyUnicode_AsUTF8(result); > | ^~~~~~~~~~~~~~~~ >x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib -lmodeller -lglib-2.0 -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/lib/_modeller.cpython-38-x86_64-linux-gnu.so > * python3_9: running distutils-r1_run_phase python_compile >python3.9 setup.py build -j 16 >running build >running build_ext >building '_modeller' extension >creating /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9 >x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -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/lib/glib-2.0/include -I/usr/include/python3.9 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9/modeller_wrap.o >modeller_wrap.c: In function 'python_cb_fangle': >modeller_wrap.c:3206:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3206 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3235:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3235 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3265:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3265 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3309:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3309 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3367:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3367 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3405:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3405 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3454:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3454 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3503:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3503 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3539:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3539 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3559:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3559 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:3583:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] > 3583 | result = PyEval_CallObject(func, arglist); > | ^~~~~~ >In file included from /usr/include/python3.9/Python.h:140, > from modeller_wrap.c:154: >/usr/include/python3.9/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:4319:18: warning: initialization discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] > 4319 | char *utf8 = PyUnicode_AsUTF8(result); > | ^~~~~~~~~~~~~~~~ >x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib -lmodeller -lglib-2.0 -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/lib/_modeller.cpython-39-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_8: running distutils-r1_run_phase python_install >python3.8 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8 >running install >running install_lib >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8 >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8 >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages >copying /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/lib/_modeller.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages >running install_egg_info >Writing /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages/Modeller-0.0.0-py3.8.egg-info > * python3_9: running distutils-r1_run_phase python_install >python3.9 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9 >running install >running install_lib >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9 >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9 >creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages >copying /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/lib/_modeller.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages >running install_egg_info >Writing /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages/Modeller-0.0.0-py3.9.egg-info > * Using python3.9 in global scope > * python3_9: running distutils-r1_run_phase python_install_all > * python3_8: running python_domodule modlib/modeller > * python3_9: running python_domodule modlib/modeller > * python3_8: running python_doscript bin/modslave.py > * python3_9: 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: 150004 KiB (146.4 MiB) > * Final size of installed tree: 64204 KiB ( 62.6 MiB) > > * QA Notice: Unresolved soname dependencies: > * > * /opt/modeller/bin/mod9.25_x86_64-intel8: libc.so.6 > * /opt/modeller/lib/x86_64-intel8/libhdf5.so.103: libc.so.6 libdl.so.2 libm.so.6 librt.so.1 > * /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.100: libc.so.6 libdl.so.2 libm.so.6 librt.so.1 > * /opt/modeller/lib/x86_64-intel8/libifcore.so.5: libc.so.6 libm.so.6 > * /opt/modeller/lib/x86_64-intel8/libimf.so: libc.so.6 > * /opt/modeller/lib/x86_64-intel8/libintlc.so.5: libc.so.6 > * /opt/modeller/lib/x86_64-intel8/libmodeller.so.12: libc.so.6 libdl.so.2 > * /opt/modeller/lib/x86_64-intel8/libpython2.3.so.1.0: libc.so.6 libdl.so.2 libm.so.6 libpthread.so.0 libutil.so.1 > * /opt/modeller/lib/x86_64-intel8/libsaxs.so: libc.so.6 > * /opt/modeller/lib/x86_64-intel8/libsvml.so: libc.so.6 > * > * Verifying compiled files in /usr/lib/python3.8/site-packages > * Verifying compiled files in /usr/lib/python3.9/site-packages >strip: x86_64-gentoo-linux-musl-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version > /usr/lib/python3.8/site-packages/_modeller.cpython-38-x86_64-linux-gnu.so > /opt/modeller/lib/x86_64-intel8/libintlc.so.5 > /opt/modeller/lib/x86_64-intel8/libsaxs.so > /opt/modeller/lib/x86_64-intel8/libsvml.so > /usr/lib/python3.9/site-packages/_modeller.cpython-39-x86_64-linux-gnu.so > /opt/modeller/lib/x86_64-intel8/libifcore.so.5 > /opt/modeller/lib/x86_64-intel8/libimf.so >>>> 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.
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