Hi, I wonder why attempt to emerge sci-biology/gatk results in so many packages picked into dependencies. I started with a gentoo docker image and I think this type of portage tree tests could be done more often by somebody better skilled with interpreting the graphs. I think the most problem-causing ebuilds are dev-java/icedtea-bin-3.10.0-r1 and x11-libs/gtk+-3.24.1. $ docker run -it gentoo/stage3-amd64-nomultilib $ docker create -v /usr/portage --name latestportagesnapshot $ docker run --volumes-from latestportagesnapshot -it gentoo/stage3-amd64-nomultilib /bin/bash dc6a36390316 / # USE="-alsa -cups -gtk -introspection -webstart -xinerama -X" emerge -pv gatk --tree These are the packages that would be merged, in reverse order: Calculating dependencies... done! [ebuild N ~] sci-biology/gatk-2.4::gentoo 8894 KiB [ebuild N ] virtual/jre-1.8.0-r1:1.8::gentoo 0 KiB [ebuild N ] dev-java/ant-core-1.10.5-r1::gentoo USE="-doc -source" 4367 KiB [ebuild N ] virtual/jdk-1.8.0-r3:1.8::gentoo 0 KiB [ebuild N ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="-alsa (-big-endian) -cups -doc -examples -gtk -headless-awt (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" 60611 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="-alsa (-big-endian) -cups -doc -examples -gtk -headless-awt (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [nomerge ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" [ebuild N ] app-eselect/eselect-fontconfig-1.1-r1::gentoo 2 KiB [ebuild N ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" 1661 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="-alsa (-big-endian) -cups -doc -examples -gtk -headless-awt (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [nomerge ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" [ebuild N ] x11-misc/shared-mime-info-1.10::gentoo USE="-test" 603 KiB [ebuild N ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" 6636 KiB [ebuild N ] virtual/jpeg-62:62::gentoo 0 KiB [ebuild N ] media-libs/libjpeg-turbo-1.5.3-r2::gentoo USE="-java -static-libs" 1635 KiB [ebuild N ] dev-lang/nasm-2.14.02::gentoo USE="-doc" 809 KiB [ebuild N ] x11-libs/libXtst-1.2.3-r1::gentoo USE="-doc -static-libs" 315 KiB [ebuild N ] x11-libs/libXrender-0.9.10-r1::gentoo USE="-static-libs" 302 KiB [ebuild N ] x11-libs/libXcomposite-0.4.4-r2::gentoo USE="-doc -static-libs" 278 KiB [ebuild N ] x11-libs/libXi-1.7.9-r1::gentoo USE="-doc -static-libs" 475 KiB [ebuild N ] x11-libs/libXfixes-5.0.3-r1::gentoo USE="-static-libs" 288 KiB [ebuild N ] x11-libs/libXext-1.3.3-r1::gentoo USE="-doc -static-libs" 381 KiB [ebuild N ] x11-libs/libX11-1.6.7::gentoo USE="ipv6 -doc -static-libs -test" 2237 KiB [ebuild N ] x11-libs/libxcb-1.13.1:0/1.12::gentoo USE="-doc (-selinux) -static-libs -test -xkb" 495 KiB [ebuild N ] x11-base/xcb-proto-1.13::gentoo PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 149 KiB [ebuild N ] virtual/ttf-fonts-1-r1::gentoo 0 KiB [ebuild N ] media-fonts/liberation-fonts-2.00.1-r3::gentoo USE="-X -fontforge" 2233 KiB [nomerge ] x11-libs/libxcb-1.13.1:0/1.12::gentoo USE="-doc (-selinux) -static-libs -test -xkb" [ebuild N ] x11-libs/libXdmcp-1.1.2-r2::gentoo USE="-doc -static-libs" 324 KiB [ebuild N ] x11-libs/libXau-1.0.8-r1::gentoo USE="-static-libs" 289 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="-alsa (-big-endian) -cups -doc -examples -gtk -headless-awt (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [nomerge ] x11-libs/libX11-1.6.7::gentoo USE="ipv6 -doc -static-libs -test" [ebuild N ] media-fonts/font-util-1.3.1::gentoo 150 KiB [ebuild N ] x11-libs/xtrans-1.3.5::gentoo USE="-doc" 183 KiB [ebuild N ] media-libs/freetype-2.9.1-r3:2::gentoo USE="adobe-cff bzip2 cleartype_hinting -X -bindist -debug -doc -fontforge -harfbuzz -infinality -png -static-libs -utils" 1882 KiB [nomerge ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" [ebuild N ] dev-util/glib-utils-2.58.3::gentoo PYTHON_SINGLE_TARGET="python3_6 -python3_5 (-python3_7)" PYTHON_TARGETS="python3_6 -python3_5 (-python3_7)" 0 KiB [nomerge ] x11-libs/libXdmcp-1.1.2-r2::gentoo USE="-doc -static-libs" [ebuild N ] dev-libs/libbsd-0.9.1::gentoo USE="-static-libs" 379 KiB [nomerge ] x11-libs/libxcb-1.13.1:0/1.12::gentoo USE="-doc (-selinux) -static-libs -test -xkb" [ebuild N ] dev-libs/libpthread-stubs-0.4-r1::gentoo 57 KiB [nomerge ] x11-libs/libXtst-1.2.3-r1::gentoo USE="-doc -static-libs" [nomerge ] x11-libs/libX11-1.6.7::gentoo USE="ipv6 -doc -static-libs -test" [ebuild N ] x11-misc/util-macros-1.19.2-r1::gentoo 83 KiB [ebuild N ] x11-base/xorg-proto-2018.4::gentoo 483 KiB [ebuild N ] dev-util/meson-0.49.2::gentoo USE="-test" PYTHON_TARGETS="python3_6 -python3_5 (-python3_7)" 1310 KiB [ebuild N ] dev-util/ninja-1.8.2::gentoo USE="-doc -emacs -test -vim-syntax" 181 KiB [ebuild N ] dev-util/re2c-1.1.1::gentoo 5769 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="-alsa (-big-endian) -cups -doc -examples -gtk -headless-awt (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [ebuild N ] app-eselect/eselect-java-0.4.0::gentoo 14 KiB [ebuild N ] media-libs/libpng-1.6.35-r1:0/16::gentoo USE="-apng (-neon) -static-libs" CPU_FLAGS_X86="sse" 991 KiB [ebuild N ] media-libs/giflib-5.1.4:0/7::gentoo USE="-doc -static-libs" 625 KiB [ebuild N ] media-libs/lcms-2.9:2::gentoo USE="threads -doc -jpeg -static-libs -test -tiff" 10698 KiB [ebuild N ] dev-java/java-config-2.2.0-r4:2::gentoo USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 51 KiB [ebuild N ] sys-apps/baselayout-java-0.1.0::gentoo 71 KiB [nomerge ] sci-biology/gatk-2.4::gentoo [ebuild N ] dev-java/javatoolkit-0.3.0-r9::gentoo PYTHON_TARGETS="python2_7" 17 KiB Total: 43 packages (43 new), Size of downloads: 115908 KiB The following keyword changes are necessary to proceed: (see "package.accept_keywords" in the portage(5) man page for more details) # required by gatk (argument) =sci-biology/gatk-2.4 ~amd64 * IMPORTANT: 14 news items need reading for repository 'gentoo'. * Use eselect news read to view new items. dc6a36390316 / # Are the X packages really necessary? dc6a36390316 / # emerge --info Portage 2.3.62 (python 3.6.5-final-0, default/linux/amd64/17.0/no-multilib, gcc-8.2.0, glibc-2.28-r6, 5.0.7-default-pciehp x86_64) ================================================================= System uname: Linux-5.0.7-default-pciehp-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.6 KiB Mem: 16363424 total, 1856692 free KiB Swap: 26853460 total, 26853460 free Timestamp of repository gentoo: Fri, 12 Apr 2019 00:45:01 +0000 Head commit of repository gentoo: 3dbc37a8acc6ff9ebeef53461f727c5bef2ba5bf sh bash 4.4_p23-r1 ld GNU ld (Gentoo 2.31.1 p5) 2.31.1 app-shells/bash: 4.4_p23-r1::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.6.5::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/openrc: 0.38.3-r1::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.69-r4::gentoo sys-devel/automake: 1.16.1-r1::gentoo sys-devel/binutils: 2.31.1-r4::gentoo sys-devel/gcc: 8.2.0-r6::gentoo sys-devel/gcc-config: 2.0::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 4.14-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.28-r6::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-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" 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/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" PKGDIR="/usr/portage/packages" 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" USE="acl amd64 berkdb bzip2 cli crypt cxx dri fortran gdbm iconv ipv6 libtirpc ncurses nls nptl openmp pam pcre readline seccomp ssl tcpd unicode xattr zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-1" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS dc6a36390316 / #
Created attachment 572682 [details] various emerge outputs
(In reply to Martin Mokrejš from comment #0) > dc6a36390316 / # USE="-alsa -cups -gtk -introspection -webstart -xinerama > -X" emerge -pv gatk --tree Try adding headless-awt to your USE flags.
yep, try enabling headless-awt useflag, it will skip a lot X/gui deps.
Created attachment 573390 [details] USE="-headless-awt" emerge -pv gatk --tree Is this any better?
Created attachment 573392 [details] USE="-headless-awt -alsa -cups -gtk -introspection -webstart -xinerama -X" emerge -pv gatk --tree Or this?
Ah, damn, I am too tired evidently. # USE="headless-awt -alsa -cups -gtk -introspection -webstart -xinerama -X" emerge -pv gatk --tree These are the packages that would be merged, in reverse order: Calculating dependencies... done! [ebuild N ~] sci-biology/gatk-2.4::gentoo 8894 KiB [ebuild N ] virtual/jre-1.8.0-r1:1.8::gentoo 0 KiB [ebuild N ] dev-java/ant-core-1.10.5-r1::gentoo USE="-doc -source" 4367 KiB [ebuild N ] virtual/jdk-1.8.0-r3:1.8::gentoo 0 KiB [ebuild N ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="headless-awt -alsa (-big-endian) -cups -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" 60611 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="headless-awt -alsa (-big-endian) -cups -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [nomerge ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" [ebuild N ] app-eselect/eselect-fontconfig-1.1-r1::gentoo 2 KiB [ebuild N ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" 1661 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="headless-awt -alsa (-big-endian) -cups -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [nomerge ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" [ebuild N ] x11-misc/shared-mime-info-1.10::gentoo USE="-test" 603 KiB [ebuild N ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" 6636 KiB [ebuild N ] virtual/jpeg-62:62::gentoo 0 KiB [ebuild N ] media-libs/libjpeg-turbo-1.5.3-r2::gentoo USE="-java -static-libs" 1635 KiB [ebuild N ] dev-lang/nasm-2.14.02::gentoo USE="-doc" 809 KiB [ebuild N ] virtual/ttf-fonts-1-r1::gentoo 0 KiB [ebuild N ] media-fonts/liberation-fonts-2.00.1-r3::gentoo USE="-X -fontforge" 2233 KiB [ebuild N ] media-libs/freetype-2.9.1-r3:2::gentoo USE="adobe-cff bzip2 cleartype_hinting -X -bindist -debug -doc -fontforge -harfbuzz -infinality -png -static-libs -utils" 1882 KiB [nomerge ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" [ebuild N ] dev-util/glib-utils-2.58.3::gentoo PYTHON_SINGLE_TARGET="python3_6 -python3_5 (-python3_7)" PYTHON_TARGETS="python3_6 -python3_5 (-python3_7)" 0 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="headless-awt -alsa (-big-endian) -cups -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source -webstart" [ebuild N ] app-eselect/eselect-java-0.4.0::gentoo 14 KiB [ebuild N ] media-libs/lcms-2.9:2::gentoo USE="threads -doc -jpeg -static-libs -test -tiff" 10698 KiB [ebuild N ] dev-java/java-config-2.2.0-r4:2::gentoo USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 51 KiB [ebuild N ] sys-apps/baselayout-java-0.1.0::gentoo 71 KiB [nomerge ] sci-biology/gatk-2.4::gentoo [ebuild N ] dev-java/javatoolkit-0.3.0-r9::gentoo PYTHON_TARGETS="python2_7" 17 KiB Total: 21 packages (21 new), Size of downloads: 100175 KiB The following keyword changes are necessary to proceed: (see "package.accept_keywords" in the portage(5) man page for more details) # required by gatk (argument) =sci-biology/gatk-2.4 ~amd64 But how am I supposed to learned to about trick? How is portage output helpful in this? Why isn't USE=-X not enough?
85bed971166f / # USE="headless-awt" emerge -pv gatk --tree These are the packages that would be merged, in reverse order: Calculating dependencies... done! The following keyword changes are necessary to proceed: (see "package.accept_keywords" in the portage(5) man page for more details) # required by gatk (argument) =sci-biology/gatk-2.4 ~amd64 !!! The ebuild selected to satisfy "dev-java/icedtea-bin:8" has unmet requirements. - dev-java/icedtea-bin-3.10.0-r1::gentoo USE="alsa cups gtk headless-awt webstart (-big-endian) -doc -examples (-multilib) -nsplugin -pulseaudio (-selinux) -source" The following REQUIRED_USE flag constraints are unsatisfied: gtk? ( !headless-awt ) The above constraints are a subset of the following complete expression: gtk? ( !headless-awt ) nsplugin? ( !headless-awt ) (dependency required by "virtual/jdk-1.8.0-r3::gentoo" [ebuild]) (dependency required by "dev-java/ant-core-1.10.5-r1::gentoo" [ebuild]) (dependency required by "sci-biology/gatk-2.4::gentoo" [ebuild]) (dependency required by "gatk" [argument]) Hmm, somewhat: 85bed971166f / # USE="headless-awt -gtk" emerge -pv gatk --tree These are the packages that would be merged, in reverse order: Calculating dependencies... done! [ebuild N ~] sci-biology/gatk-2.4::gentoo 8894 KiB [ebuild N ] dev-java/ant-core-1.10.5-r1::gentoo USE="-doc -source" 4367 KiB [nomerge ] dev-java/ant-core-1.10.5-r1::gentoo USE="-doc -source" [nomerge ] virtual/jdk-1.8.0-r3:1.8::gentoo [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [ebuild N ] dev-java/icedtea-web-1.6.2::gentoo USE="-doc -javascript -nsplugin -tagsoup -test" 1782 KiB [ebuild N ] virtual/jre-1.8.0-r1:1.8::gentoo 0 KiB [ebuild N ] virtual/jdk-1.8.0-r3:1.8::gentoo 0 KiB [ebuild N ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" 60611 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [nomerge ] net-print/cups-2.2.7::gentoo USE="acl pam ssl threads -X -dbus -debug -java -kerberos -lprng-compat -python (-selinux) -static-libs -systemd -usb -xinetd -zeroconf" PYTHON_TARGETS="python2_7" [ebuild N ] net-print/cups-filters-1.21.6::gentoo USE="foomatic postscript -dbus -ipp_autosetup -jpeg -ldap -pclm -pdf -perl -png -static-libs -test -tiff -zeroconf" 1441 KiB [ebuild N ] app-text/ghostscript-gpl-9.26::gentoo USE="cups unicode -X -dbus -gtk -static-libs -tiff" L10N="-de -ja -ko -zh-CN -zh-TW" 32289 KiB [ebuild N ] net-print/cups-2.2.7::gentoo USE="acl pam ssl threads -X -dbus -debug -java -kerberos -lprng-compat -python (-selinux) -static-libs -systemd -usb -xinetd -zeroconf" PYTHON_TARGETS="python2_7" 10089 KiB [ebuild N ] dev-util/gdbus-codegen-2.58.3::gentoo PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_5 (-python3_7)" PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 4750 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [nomerge ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" [ebuild N ] x11-misc/shared-mime-info-1.10::gentoo USE="-test" 603 KiB [ebuild N ] dev-libs/glib-2.58.3:2::gentoo USE="mime xattr -dbus -debug (-fam) -gtk-doc (-selinux) -static-libs -systemtap -test -utils" 1886 KiB [nomerge ] net-print/cups-filters-1.21.6::gentoo USE="foomatic postscript -dbus -ipp_autosetup -jpeg -ldap -pclm -pdf -perl -png -static-libs -test -tiff -zeroconf" [ebuild N ] app-text/poppler-0.74.0:0/85::gentoo USE="cxx introspection jpeg jpeg2k lcms utils -cairo -cjk -curl -debug -doc -nss -png -qt5 -tiff" 1479 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [nomerge ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" [ebuild N ] app-eselect/eselect-fontconfig-1.1-r1::gentoo 2 KiB [ebuild N ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" 1661 KiB [ebuild N ] virtual/jpeg-62:62::gentoo 0 KiB [nomerge ] app-text/ghostscript-gpl-9.26::gentoo USE="cups unicode -X -dbus -gtk -static-libs -tiff" L10N="-de -ja -ko -zh-CN -zh-TW" [ebuild N ] media-libs/openjpeg-2.3.0-r1:2/7::gentoo USE="-doc -static-libs -test" 2156 KiB [ebuild N ] dev-util/cmake-3.9.6::gentoo USE="ncurses -doc -emacs -qt5 -server -system-jsoncpp -test" 7525 KiB [ebuild N ] app-arch/libarchive-3.3.1:0/13::gentoo USE="acl bzip2 e2fsprogs iconv lzma threads xattr zlib -expat -libressl -lz4 -lzo -nettle -static-libs" 6075 KiB [nomerge ] net-print/cups-filters-1.21.6::gentoo USE="foomatic postscript -dbus -ipp_autosetup -jpeg -ldap -pclm -pdf -perl -png -static-libs -test -tiff -zeroconf" [ebuild N ] sys-devel/bc-1.06.95-r2::gentoo USE="readline -libedit -static" 284 KiB [ebuild N ] app-text/qpdf-8.2.1:0/21::gentoo USE="-doc -examples -perl -static-libs -test" 8063 KiB [ebuild N ] virtual/jpeg-0-r3::gentoo USE="-static-libs" 0 KiB [ebuild N ] media-libs/libjpeg-turbo-1.5.3-r2::gentoo USE="-java -static-libs" 1635 KiB [ebuild N ] dev-lang/nasm-2.14.02::gentoo USE="-doc" 809 KiB [nomerge ] net-print/cups-filters-1.21.6::gentoo USE="foomatic postscript -dbus -ipp_autosetup -jpeg -ldap -pclm -pdf -perl -png -static-libs -test -tiff -zeroconf" [nomerge ] media-libs/fontconfig-2.13.0-r4:1.0::gentoo USE="-doc -static-libs" [ebuild N ] virtual/ttf-fonts-1-r1::gentoo 0 KiB [ebuild N ] media-fonts/liberation-fonts-2.00.1-r3::gentoo USE="-X -fontforge" 2233 KiB [ebuild N ] media-libs/freetype-2.9.1-r3:2::gentoo USE="adobe-cff bzip2 cleartype_hinting -X -bindist -debug -doc -fontforge -harfbuzz -infinality -png -static-libs -utils" 1882 KiB [nomerge ] app-text/poppler-0.74.0:0/85::gentoo USE="cxx introspection jpeg jpeg2k lcms utils -cairo -cjk -curl -debug -doc -nss -png -qt5 -tiff" [ebuild N ] dev-util/ninja-1.8.2::gentoo USE="-doc -emacs -test -vim-syntax" 181 KiB [ebuild N ] dev-util/re2c-1.1.1::gentoo 5769 KiB [nomerge ] app-text/poppler-0.74.0:0/85::gentoo USE="cxx introspection jpeg jpeg2k lcms utils -cairo -cjk -curl -debug -doc -nss -png -qt5 -tiff" [nomerge ] dev-util/cmake-3.9.6::gentoo USE="ncurses -doc -emacs -qt5 -server -system-jsoncpp -test" [ebuild N ] app-crypt/rhash-1.3.6-r1::gentoo USE="nls ssl -debug -libressl -static-libs" 321 KiB [nomerge ] app-text/poppler-0.74.0:0/85::gentoo USE="cxx introspection jpeg jpeg2k lcms utils -cairo -cjk -curl -debug -doc -nss -png -qt5 -tiff" [nomerge ] media-libs/openjpeg-2.3.0-r1:2/7::gentoo USE="-doc -static-libs -test" [ebuild N ] media-libs/tiff-4.0.10::gentoo USE="cxx zlib -jbig -jpeg -lzma -static-libs -test -webp -zstd" 2347 KiB [nomerge ] app-text/ghostscript-gpl-9.26::gentoo USE="cups unicode -X -dbus -gtk -static-libs -tiff" L10N="-de -ja -ko -zh-CN -zh-TW" [ebuild N ] media-fonts/urw-fonts-2.4.9::gentoo USE="-X" 3124 KiB [ebuild N ] app-arch/rpm2targz-9.0.0.5g::gentoo 6 KiB [ebuild N ] app-arch/cpio-2.12-r1::gentoo USE="nls" 1230 KiB [ebuild N ] app-text/poppler-data-0.4.9::gentoo 4099 KiB [ebuild N ] net-dns/libidn-1.35:0/12::gentoo USE="nls -doc -emacs -java -mono -static-libs" 4072 KiB [ebuild N ] media-libs/jbig2dec-0.13-r4::gentoo USE="-png -static-libs -test" 441 KiB [nomerge ] dev-java/icedtea-web-1.6.2::gentoo USE="-doc -javascript -nsplugin -tagsoup -test" [ebuild N ] app-arch/zip-3.0-r3::gentoo USE="bzip2 crypt unicode -natspec" 1258 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [ebuild N ] media-libs/alsa-lib-1.1.8::gentoo USE="thread-safety -alisp -debug -doc -python" PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_5 (-python3_7)" PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 980 KiB [ebuild N ] dev-java/java-config-2.2.0-r4:2::gentoo USE="-test" PYTHON_TARGETS="python2_7 python3_6 -python3_5 (-python3_7)" 51 KiB [ebuild N ] sys-apps/baselayout-java-0.1.0::gentoo 71 KiB [nomerge ] app-text/poppler-0.74.0:0/85::gentoo USE="cxx introspection jpeg jpeg2k lcms utils -cairo -cjk -curl -debug -doc -nss -png -qt5 -tiff" [ebuild N ] dev-util/glib-utils-2.58.3::gentoo PYTHON_SINGLE_TARGET="python3_6 -python3_5 (-python3_7)" PYTHON_TARGETS="python3_6 -python3_5 (-python3_7)" 0 KiB [nomerge ] app-text/ghostscript-gpl-9.26::gentoo USE="cups unicode -X -dbus -gtk -static-libs -tiff" L10N="-de -ja -ko -zh-CN -zh-TW" [ebuild N ] media-libs/libpng-1.6.35-r1:0/16::gentoo USE="-apng (-neon) -static-libs" CPU_FLAGS_X86="sse" 991 KiB [ebuild N ] app-text/libpaper-1.1.24-r2::gentoo 347 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [ebuild N ] app-eselect/eselect-java-0.4.0::gentoo 14 KiB [nomerge ] sci-biology/gatk-2.4::gentoo [ebuild N ] dev-java/javatoolkit-0.3.0-r9::gentoo PYTHON_TARGETS="python2_7" 17 KiB [nomerge ] dev-java/icedtea-bin-3.10.0-r1:8::gentoo USE="alsa cups headless-awt webstart (-big-endian) -doc -examples -gtk (-multilib) -nsplugin -pulseaudio (-selinux) -source" [ebuild N ] media-libs/lcms-2.9:2::gentoo USE="threads -doc -jpeg -static-libs -test -tiff" 10698 KiB Total: 47 packages (47 new), Size of downloads: 196512 KiB The following keyword changes are necessary to proceed: (see "package.accept_keywords" in the portage(5) man page for more details) # required by gatk (argument) =sci-biology/gatk-2.4 ~amd64 The following USE changes are necessary to proceed: (see "package.use" in the portage(5) man page for more details) # required by net-print/cups-filters-1.21.6::gentoo[postscript] # required by net-print/cups-2.2.7::gentoo # required by dev-java/icedtea-bin-3.10.0-r1::gentoo[cups] # required by virtual/jdk-1.8.0-r3::gentoo # required by sci-biology/gatk-2.4::gentoo # required by gatk (argument) >=app-text/ghostscript-gpl-9.26 cups
please seek support on gentoo forums or #gentoo channel on freenode, this is not a bug, it's a support question. I can read and comprehend portage output just fine, takes time to learn. if you enable headless-awt, gtk useflag can't be enabled. in last output it's cups pulling in a lot of deps. basically you want headless-awt -gtk -cups -webstart useflag descriptions are also can be useful # grep headless-awt "$(portageq get_repo_path / gentoo)"/profiles/use.local.desc dev-java/icedtea-bin:headless-awt - Don't install the X backend for AWT, needed by some GUIs (used to be X flag) historically headless-awt used to be X flag, but it was renamed due to valid reasons. USE="-alsa -cups -gtk -webstart -doc -examples -nsplugin -pulseaudio -source headless-awt" emerge --oneshot --ask icedtea-bin and install gatk after that.
