[Note: according due to the below quoted outputs, emerge --sync 40d ago... however, problem arose during prefix bootstrapping today... nothing 40d ago] From output of bootstrap-prefix.sh script: Odd! Running /usr/bin/bash ./bootstrap-prefix.sh "/cygdrive/c/gentooprefix" stage2 failed! :( Details might be found in the build log: /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/temp/build.log (no build logs found?!?) $ tmp/usr/bin/emerge --info =app-arch/unzip-6.0_p20::gentoo_prefix Portage 2.3.5-prefix (python 2.7.3-final-0, prefix/windows/cygwin/x64, gcc-5.4.0, unavailable, 2.8.2-gentoo-r0 x86_64) ================================================================= System Settings ================================================================= System uname: CYGWIN_NT-6.3-2.8.2-gentoo-r0-x86_64-64bit Timestamp of repository gentoo_prefix: Sat, 08 Jul 2017 21:58:19 +0000 sh bash 4.3_p48 ld GNU ld (GNU Binutils) 2.25.2 app-shells/bash: 4.3_p48::gentoo_prefix sys-devel/binutils: 2.27::gentoo_prefix sys-devel/gcc-config: 1.8-r01.1::gentoo_prefix Repositories: gentoo_prefix location: /cygdrive/c/gentooprefix/usr/portage sync-type: rsync sync-uri: rsync://rsync.prefix.bitzolder.nl/gentoo-portage-prefix priority: -1000 ACCEPT_KEYWORDS="~x64-cygwin" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-cygwin" CFLAGS=" -O2 -pipe" CHOST="x86_64-pc-cygwin" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/gentoo-release /etc/terminfo" CXXFLAGS=" -O2 -pipe" DISTDIR="/cygdrive/c/gentooprefix/tmp/usr/portage/distfiles" FCFLAGS="" FEATURES="assume-digests binpkg-logs case-insensitive-fs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="" MAKEOPTS="-j3" PKGDIR="/cygdrive/c/gentooprefix/tmp/usr/portage/packages" PORTAGE_CONFIGROOT="/cygdrive/c/gentooprefix/tmp/" 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="/cygdrive/c/gentooprefix/tmp/var/tmp" USE="cracklib cxx modules ncurses nls prefix prefix-guest readline ssl unicode x64-cygwin zlib" 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="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="Cygwin" 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="keyboard mouse" KERNEL="Winnt" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby22 ruby24" USERLAND="GNU" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON $ tmp/usr/bin/emerge -pqv =app-arch/unzip-6.0_p20::gentoo_prefix * Last emerge --sync was 40d 16h 12m 50s ago. [ebuild N ] app-arch/unzip-6.0_p20 USE="unicode -bzip2 -natspec" $ cat tmp/var/tmp/portage/app-arch/unzip-6.0_p20/temp/build.log * Package: app-arch/unzip-6.0_p20 * Repository: gentoo_prefix * USE: elibc_Cygwin kernel_Winnt prefix prefix-guest unicode userland_GNU x64-cygwin * FEATURES: nostrip preserve-libs >>> Unpacking source... >>> Unpacking unzip60.tar.gz to /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work >>> Unpacking unzip_6.0-20.debian.tar.xz to /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work >>> Source unpacked in /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work >>> Preparing source in /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60 ... * Applying 01-manpages-in-section-1-not-in-section-1l ... [ ok ] * Applying 03-include-unistd-for-kfreebsd ... [ ok ] * Applying 04-handle-pkware-verification-bit ... [ ok ] * Applying 05-fix-uid-gid-handling ... [ ok ] * Applying 06-initialize-the-symlink-flag ... [ ok ] * Applying 07-increase-size-of-cfactorstr ... [ ok ] * Applying 08-allow-greater-hostver-values ... [ ok ] * Applying 09-cve-2014-8139-crc-overflow ... [ ok ] * Applying 10-cve-2014-8140-test-compr-eb ... [ ok ] * Applying 11-cve-2014-8141-getzip64data ... [ ok ] * Applying 12-cve-2014-9636-test-compr-eb ... [ ok ] * Applying 13-remove-build-date ... [ ok ] * Applying 14-cve-2015-7696 ... [ ok ] * Applying 15-cve-2015-7697 ... [ ok ] * Applying 16-fix-integer-underflow-csiz-decrypted ... [ ok ] * Applying unzip-6.0-no-exec-stack.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60 ... >>> Source configured. >>> Compiling source in /cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60 ... make SHELL=/cygdrive/c/gentooprefix/tmp/bin/bash -j3 -f unix/Makefile cygwin make unzips CC="gcc" LD="gcc" AS="gcc"\ CFLAGS=" -O2 -pipe -I/cygdrive/c/gentooprefix/tmp/usr/include -DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DLARGE_FILE_SUPPORT -DASM_CRC -DNO_LCHOWN -DNO_LCHMOD"\ AF="-Di386 " CRCA_O=crc_gcc.o\ E=".exe" CP="cp" LN="ln -s" make[1]: Entering directory '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60' gcc -c -O2 -pipe -I/cygdrive/c/gentooprefix/tmp/usr/include -DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DLARGE_FILE_SUPPORT -DASM_CRC -DNO_LCHOWN -DNO_LCHMOD -I. -Ibzip2 -DUNIX unzip.c gcc -c -O2 -pipe -I/cygdrive/c/gentooprefix/tmp/usr/include -DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DLARGE_FILE_SUPPORT -DASM_CRC -DNO_LCHOWN -DNO_LCHMOD -I. -Ibzip2 -DUNIX crc32.c gcc -Di386 -x assembler-with-cpp -c -o crc_gcc.o crc_i386.S crc_i386.S: Assembler messages: crc_i386.S:203: Error: invalid instruction suffix for `push' crc_i386.S:204: Error: invalid instruction suffix for `push' crc_i386.S:205: Error: invalid instruction suffix for `push' crc_i386.S:206: Error: invalid instruction suffix for `push' crc_i386.S:207: Error: invalid instruction suffix for `push' crc_i386.S:208: Error: invalid instruction suffix for `push' crc_i386.S:292: Error: invalid instruction suffix for `pop' crc_i386.S:293: Error: invalid instruction suffix for `pop' crc_i386.S:294: Error: invalid instruction suffix for `pop' crc_i386.S:295: Error: invalid instruction suffix for `pop' crc_i386.S:296: Error: invalid instruction suffix for `pop' crc_i386.S:297: Error: invalid instruction suffix for `pop' make[1]: *** [Makefile:379: crc_gcc.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60' make: *** [unix/Makefile:747: cygwin] Error 2 * ERROR: app-arch/unzip-6.0_p20::gentoo_prefix failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=app-arch/unzip-6.0_p20::gentoo_prefix'`, * the complete build log and the output of `emerge -pqv '=app-arch/unzip-6.0_p20::gentoo_prefix'`. * The complete build log is located at '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/temp/build.log'. * The ebuild environment file is located at '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/temp/environment'. * Working directory: '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60' * S: '/cygdrive/c/gentooprefix/tmp/var/tmp/portage/app-arch/unzip-6.0_p20/work/unzip60'
This should already be fixed in https://gitweb.gentoo.org/repo/proj/prefix.git/commit/?id=bec2b5364c3626a935d37a43fc031ae3091b0054, but the tree snapshot used probably is older. Does it work for you when you start over with LATEST_TREE_YES=1 environment variable set?