port selfupdate failed: Couldn't sync the ports tree: Synchronization of 1 source(s) failed

[michaelwallis@…]

Not sure what changed, but I'm having trouble updating ports. I reinstalled the Yosemite MacPorts but I still get:

$ sudo port -v selfupdate ---> Updating MacPorts base sources using rsync receiving file list ... done

sent 36 bytes received 30250 bytes 60572.00 bytes/sec total size is 25420143 speedup is 839.34 MacPorts base version 2.3.4 installed, MacPorts base version 2.3.4 downloaded. ---> Updating the ports tree Synchronizing local ports tree from rsync://rsync.macports.org/release/ports/ receiving file list ... rsync: readlink_stat("/ports/devel/libatomic_ops/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/devel/xxl/files/patch-configure.ac.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/devel/crlibm/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/mail/sympa/files/httpd-sympa.conf" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/kde/kde-l10n-eu/files/patch-CMakeLists.txt.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/gadap/files/patch-gaBaseTypes.h.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/h5utils/files/patch-writepng.c" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/gqrx/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/libghemical/files/patch-autogen.sh.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/armadillo/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/viking/files/autogen.sh" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/ghemical/files/patch-autogen.sh.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/hdf5/files/yosemite-libtool.patch" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/bedtools/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/swarm/files/patch-libpng-1.5.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/science/ldas-tools/files/patch-libraries-ldastoolsal-src-AtExit.cc.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/audio/sptk/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/textproc/unicode/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/sysutils/augeas/files/yosemite-libtool.patch" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/sysutils/libfaketime/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/sysutils/sunwait/files/patch-main.c.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/tex/blahtexml/files/patch-main.cpp.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rb-pcap/files/patch-Pcap.c.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rb-rjab-connection/files/patch-conn_connection.rb" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rb-tapkit/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rbenv/files/patch-libexec-rbenv-init.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rb19-em-websocket/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/ruby/rb19-activemodel/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/aqua/qt4-mac-mysql55-plugin/Portfile" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/x11/fluxbox/files/patch-Makefile.in.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/x11/xtide/files/patch-configure.ac.diff" (in release)) failed: Input/output error (5) rsync: readlink_stat("/ports/security/pbc/files/patch-configure.diff" (in release)) failed: Input/output error (5) done archivers/advancescan/Portfile archivers/arc/Portfile archivers/arj/Portfile archivers/arj/files/patch-uxspec.c archivers/bzip2/files/patch-Makefile-man.diff archivers/dact/Portfile archivers/dzip/Portfile archivers/dzip/files/patch-Makefile.linux.diff archivers/ecm/Portfile archivers/gzip/Portfile archivers/gzrecover/files/patch-Makefile archivers/libzzip/files/patch-zzip_Makefile.in.diff archivers/pigz/files/patch-Makefile.diff archivers/ppmd/Portfile archivers/sharutils/Portfile archivers/slimdata/Portfile archivers/star/files/patch-RULESrules.prg.diff archivers/szip/Portfile archivers/zip/Portfile archivers/zlib/Portfile archivers/zoo/Portfile devel/CImg/Portfile devel/Drizzle/files/drizzle.in devel/MongoObjCDriver/Portfile devel/SilverCity/Portfile devel/aap/files/patch-python26.diff devel/apr-util0/Portfile devel/autoconf264/Portfile devel/bullet/Portfile devel/bzr-rewrite/Portfile devel/cableswig/Portfile devel/cableswig/files/no-windows-compilers.patch devel/cegui/Portfile devel/cegui/files/patch-cegui-include-CEGUIDynamicModule.h.diff devel/coccinelle/Portfile devel/curlhandle/files/patch-CURLFTPSession.m.diff devel/curlhandle/files/patch-CURLHandle.xcodeproj-project.pbxproj.diff devel/expect/Portfile devel/generatorrunner/Portfile devel/glade3/Portfile devel/glib2/Portfile devel/glib2/files/config.h.ed devel/glib2/files/patch-configure.diff devel/glib2/files/patch-glib_gunicollate.c.diff devel/gmp-cxx-wrappers/Portfile devel/gnats/Portfile devel/gnet2/Portfile devel/gtk-osx-application/Portfile devel/hs-bibutils/Portfile devel/hs-boolean/Portfile devel/hs-crypto/Portfile devel/hs-data-accessor-template/Portfile devel/hs-data-default-instances-containers/Portfile devel/hs-highlighting-kate/Portfile devel/hs-json/Portfile devel/hs-monads-fd/Portfile devel/hs-platform-async/Portfile devel/hs-platform-random/Portfile devel/hs-platform-split/Portfile devel/hs-platform-transformers/Portfile devel/hs-tf-random/Portfile devel/jam/Portfile devel/ld64/files/Makefile-127 devel/ld64/files/ld64-127-cxx_initializer_order_and_sim.patch devel/libdaemon/Portfile devel/libgdiplus/files/patch-freetype-2.5.1.diff devel/libmongo-client/Portfile devel/libmowgli/files/patch-m4-buildsys.m4.diff devel/libnotify/Portfile devel/liboil/Portfile devel/liboil/files/automake.patch devel/libproplist/files/patch-config.guess devel/libproplist/files/patch-config.sub devel/libsdl/files/include_SDL_config.h.ed devel/libtool-devel/Portfile devel/libut/Portfile devel/libut/files/prf_shl.c.patch devel/magit/Portfile devel/maloc/Portfile devel/minipro/Portfile devel/ninka/Portfile devel/ninka/files/patch-ninka_pl.diff devel/nspr/files/nspr.pc devel/nuweb/Portfile devel/ocaml-menhir/Portfile devel/pick/Portfile devel/protobuf-c/Portfile devel/protobuf-cpp/Portfile devel/rcs/Portfile devel/tailor/Portfile devel/tclsqlite2/Portfile devel/tclsqlite2/files/Makefile devel/thieriot/Portfile devel/tig/Portfile devel/udis86/Portfile devel/util-linux/Portfile devel/valgrind/Portfile devel/xml-light/Portfile devel/zshdb/Portfile emulators/dosbox/files/3776.diff emulators/gelide/files/patch-autogen.sh.diff emulators/hatari/Portfile emulators/hercules/Portfile emulators/hercules/files/patch-hscutl.c.diff emulators/lisaem/Portfile emulators/minivmac-devel/files/README-binary-patchfiles.md emulators/minivmac-devel/files/readalias.applescript emulators/minivmac/files/README-binary-patchfiles.md emulators/nonpareil/files/patch-src-util.diff emulators/nonpareil/files/patch-src-voyager.diff emulators/qemu-usermode/Portfile emulators/qemu-usermode/files/patch-configure emulators/qemu-usermode/files/patch-q-i386 emulators/qemu/Portfile emulators/qemu/files/patch-configure.diff emulators/xhyve/Portfile erlang/rebar/Portfile games/2Pong/Portfile games/2Pong/files/2Pong.in games/2Pong/files/patch-Makefile.diff games/2Pong/files/patch-defs.h.diff games/CrimsonFields/files/patch-cf-path.cpp.diff games/bluemoon/Portfile games/boswars/Portfile games/crack-attack/files/patch-glut-init.diff games/digger/files/patch-main.c.diff games/digger/files/patch-scores.c.diff games/duke3d/Portfile games/fife/Portfile games/fizmo/Portfile games/flobopuyo/Portfile games/flobopuyo/files/IosVector.cpp.patch games/flobopuyo/files/PuyoGame.cpp.patch games/gcs-java/Portfile games/gdash/files/patch-src-sdl-ogl.hpp.diff games/gtypist/Portfile games/gtypist/files/patch-src_Makefile.in-add-libiconv.diff games/lbreakout2/files/patch-gui-stk.c.diff games/mindless/Portfile games/openmortal/files/openmortal-0.7-gcc41.patch games/sdl_sopwith/Portfile games/ship84/files/patch-GNUmakefile.diff games/ship84/files/patch-shippy.c.diff games/supertuxkart/Portfile games/widelands/files/clang.patch kde/amarok/Portfile kde/amarok/files/patch-TrayIcon.diff kde/analitza/files/patch-plotter2d.diff kde/analitza/files/patch-plotter3d.diff kde/ark/Portfile kde/attica/Portfile kde/blinken/files/patch-CMakeLists.txt.diff kde/bomber/files/patch-CMakeLists.diff kde/bovo/Portfile kde/digikam/Portfile kde/dragon/Portfile kde/dragon/files/patch-CMakeLists.txt.diff kde/ffmpegthumbs/Portfile kde/granatier/Portfile kde/juk/Portfile kde/juk/files/patch-CMakeLists.txt.diff kde/kactivities/Portfile kde/kalzium/files/patch-CMakeLists.txt.diff kde/kamera/Portfile kde/kanagram/Portfile kde/kanagram/files/patch-CMakeLists.txt.diff kde/kapman/Portfile kde/kapman/files/patch-CMakeLists.diff kde/kate/Portfile kde/katomic/Portfile kde/katomic/files/patch-CMakeLists.diff kde/kblackbox/Portfile kde/kblackbox/files/patch-CMakeLists.diff kde/kblocks/files/patch-CMakeLists.diff kde/kbounce/Portfile kde/kbounce/files/patch-CMakeLists.diff kde/kbreakout/Portfile kde/kbreakout/files/patch-CMakeLists.diff kde/kbruch/Portfile kde/kbruch/files/patch-CMakeLists.txt.diff kde/kcolorchooser/files/patch-CMakeLists.diff kde/kde-extra-cmake-modules/files/patch-doc-building.diff kde/kde-l10n-ca/files/patch-CMakeLists.txt.diff kde/kde-l10n-cs/files/patch-CMakeLists.txt.diff kde/kde-l10n-el/files/patch-CMakeLists.txt.diff kde/kde-l10n-en_GB/files/patch-CMakeLists.txt.diff kde/kde-l10n-es/files/patch-CMakeLists.txt.diff kde/kde-l10n-fr/files/patch-CMakeLists.txt.diff kde/kde-l10n-uk/Portfile kde/kde-l10n-zh_CN/Portfile kde/kdepim4-runtime/files/patch-CMake-InfoPlist.diff kde/kdepim4/files/patch-blogger.diff kde/kdepim4/files/patch-emulate-addTitle.diff kde/kdepimlibs4/files/patch-CMakeLists-kioslaves.diff kde/kdepimlibs4/files/patch-CMakeLists.diff kde/kdiamond/Portfile kde/kfourinline/Portfile kde/kfourinline/files/patch-CMakeLists.diff kde/killbots/files/patch-CMakeLists.diff kde/kjumpingcube/Portfile kde/klickety/Portfile kde/klickety/files/patch-CMakeLists.diff kde/klines/files/patch-CMakeLists.diff kde/kmines/Portfile kde/kmines/files/patch-CMakeLists.diff kde/kmix/Portfile kde/kmix/files/patch-C11-headers.diff kde/kmix/files/patch-CMakeLists.txt.diff kde/knavalbattle/Portfile kde/knavalbattle/files/patch-CMakeLists.diff kde/kolf/Portfile kde/kolf/files/patch-CMakeLists.diff kde/kollision/files/patch-CMakeLists.diff kde/konquest/Portfile kde/konquest/files/patch-CMakeLists.diff kde/kpat/Portfile kde/kpat/files/patch-CMakeLists.diff kde/kreversi/Portfile kde/kreversi/files/patch-CMakeLists.diff kde/kscd/Portfile kde/kshisen/Portfile kde/kshisen/files/patch-CMakeLists.diff kde/ksirk/files/patch-CMakeLists.diff kde/ksnakeduel/Portfile kde/ksystemlog/files/patch-CMakeLists.diff kde/ktuberling/files/patch-CMakeLists.diff kde/kubrick/Portfile kde/libkcddb/Portfile kde/libkcompactdisc/Portfile kde/libkdegames/Portfile kde/libkmahjongg/Portfile kde/lskat/files/patch-CMakeLists.diff kde/mplayerthumbs/Portfile kde/nepomuk-core/files/patch-nepomuk-make-daemons-agents.diff kde/nepomuk-core/files/patch-nepomukctl.diff kde/nepomuk-widgets/Portfile kde/pairs/files/patch-Newiconfolder.diff kde/palapeli/Portfile kde/picmi/files/patch-CMakeLists.diff kde/py-pykde4/files/kubuntu_include_dirs.diff kde/py-pykde4/files/pythonpluginfactory_python3.diff kde/qtcurve/files/QtCurveOSX.colors kde/qtcurve/files/qtc_qtcurve-osx.themerc kde/qtcurve/files/qtc_qtcurve-rjvb.themerc mail/GNUMail-Aqua/Portfile mail/Pantomime-Framework/Portfile mail/Pantomime-Framework/files/Info-PantomimeUpgraded_.plist mail/Pantomime-Framework/files/project.pbxproj mail/alpine/files/patch-configure.diff mail/altermime/Portfile mail/amavisd-new/Portfile mail/anubis/Portfile mail/assp/files/patch-assp.pl.diff mail/base-64/Portfile mail/bincimap/Portfile mail/bincimap/files/README.MACOSX.in mail/bincimap/files/patch-Makefile.in.diff mail/bincimap/files/patch-service.diff mail/bogofilter/Portfile mail/cclient/Portfile mail/claws-mail/Portfile mail/courier-imap/files/patch-rfc1035_res.h mail/cyrus-imapd/Portfile mail/cyrus-imapd/files/patch-depot-Makefile.in.diff mail/cyrus5-imapd/Portfile mail/dovecot/Portfile mail/dovecot2-antispam/Portfile mail/dovecot2/Portfile mail/dspam/Portfile mail/notmuch/files/patch-bindings-python-notmuch-globals.py.diff mail/postfinger/Portfile mail/surblhost/files/patch-surblhost.c.diff mail/sympa/files/patch-src-etc-script-sympa.in.diff mail/sympa/files/patch-src-lib-confdef.pm.diff print/a2ps-j/Portfile print/a2ps/files/patch-contrib_sample_Makefile.in print/a2ps/files/patch-libxstrrpl.c print/a2ps/files/patch-ps-base.ps print/abcm2ps/files/patch-Makefile.in.diff print/cups-pdf/Portfile print/cups-pdf/files/cups-pdf_links.sh print/denemo/Portfile print/epdfview/Portfile print/epstool/Portfile print/espgs/Portfile print/fondu/Portfile print/fonttools/Portfile print/ghostscript/files/patch-base_stdpre.h.diff print/latex2html/Portfile print/lcdf-typetools/Portfile print/libLASi/Portfile print/libLASi/files/patch-freetype-2.5.1.diff print/pdflib/Portfile print/pdfposter/Portfile print/ppmtomd/Portfile print/ps2eps/Portfile print/pscal/Portfile print/rlpr/Portfile print/transfig/Portfile science/EGSimulation/Portfile science/KlustaKwik/Portfile science/KlustaKwik/files/patch-KlustaKwik-makefile.diff science/KlustaKwik/files/patch-maskedKlustaKwik-makefile.diff science/OpenCSG/Portfile science/TwitterDemandCollector/Portfile science/airspy/files/patch-disable-std-gnu90.diff science/alliance/Portfile science/alps/Portfile science/alps/files/patch-CMakeLists.txt.diff science/alps/files/patch-config-FindPython.cmake.diff science/apbs/Portfile science/ape/files/patch-src-parser_symbols.F90.diff science/arb/Portfile science/arb/files/arb_macsetup science/arb/files/patch-ARB-arb.diff science/arb/files/patch-ARB-arb_compiler_version.pl.diff science/arb/files/patch-ARB-config.makefile.diff science/arb/files/patch-ARB-globalsosx.cpp.diff science/arb/files/patch-ARB-intro.fig.diff science/arb/files/patch-Makefile.diff science/archimedes/Portfile science/berkeleygw/files/patch-testsuite-Silane-PARATEC-Silane.test.diff science/caml-camlmpi/Portfile science/caml-camlmpi/files/META science/caml-camlmpi/files/Makefile.diff science/ccpnmr/Portfile science/ccpnmr/files/ccpnmr.patch science/cdf/Portfile science/cdo/Portfile science/cdsclient/Portfile science/cdsclient/files/patch-Makefile.in science/cdsclient/files/patch-configure science/ce/Portfile science/ce/files/patch-Makefiles.diff science/ce/files/patch-nonstandardcode.diff science/cfitsio/Portfile science/cfitsio/files/patch-Makefile.in.diff science/cfitsio/files/patch-configure.diff science/cgnslib/Portfile science/clustalx/Portfile science/clustalx/files/clustalx.in science/demeter/Portfile science/demeter/files/patch-DocBuilder-Artemis.pm.diff science/demeter/files/patch-DocBuilder-Athena.pm.diff science/dineroIV/Portfile science/dineroIV/files/patch-misc_c.diff science/drc-fir/Portfile science/drc-fir/files/patch-drc.diff science/eo/Portfile science/eo/files/patch-eoBit.h.diff science/eo/files/patch-eoFileSnapshot.h.diff science/eo/files/patch-eoGnuplot.cpp.diff science/eo/files/patch-make_checkpoint.h.diff science/eo/files/patch-make_checkpoint_FDC.h.diff science/eo/files/patch-make_checkpoint_assembled.h.diff science/eo/files/patch-make_checkpoint_pareto.h.diff science/eo/files/patch-make_help.cpp.diff science/erfa/Portfile science/exonerate/Portfile science/exonerate/files/patch-src-program-Makefile.am.diff science/exonerate/files/patch-src-program-Makefile.in.diff science/eye/Portfile science/fann/Portfile science/fastcap-wr/Portfile science/fasthenry-wr/Portfile science/fastlink/Portfile science/fcl/Portfile science/flann/Portfile science/flann/files/patch-CMakeLists.txt.diff science/flann/files/patch-src-python-CMakeLists.txt.diff science/freehdl/Portfile science/freehdl/files/kernel-sig-info.hh.patch science/freehdl/files/std-vhdl-types.hh.patch science/funtools/Portfile science/funtools/files/patch-funtools science/gadap/Portfile science/gds/files/patch-config-ac_dmtoffline.m4.diff science/geant4/files/geant4.10.0 science/geant4/files/geant4.10.1 science/geant4/files/geant4.9.5 science/geant4/files/patch-cmake-Modules-Geant4BuildProjectConfig.cmake.4101.diff science/geant4/files/patch-cmake-Modules-Geant4BuildProjectConfig.cmake.495.diff science/geant4/files/patch-cmake-Modules-Geant4InterfaceOptions.cmake.4100.diff science/geant4/files/patch-cmake-Modules-Geant4InterfaceOptions.cmake.4101.diff science/geant4/files/patch-cmake-Modules-Geant4InterfaceOptions.cmake.495.diff science/geant4/files/patch-cmake-Modules-Geant4InterfaceOptions.cmake.496.diff science/geant4/files/patch-upstream-examples-advanced-xray_fluorescence.diff science/geant4/files/patch-upstream-qt.496.diff science/geant4/files/patch-upstream-source-interfaces-common-src-G4Qt.cc.495.diff science/geda-gaf/Portfile science/geoexpress-sdk/Portfile science/geomview/Portfile science/geomview/files/patch-iobuffer.c.diff science/geos/Portfile science/gerbil/Portfile science/gerbil/files/patch-lsblsbhreader.cpp-missing-include.diff science/ggobi/Portfile science/ggobi/files/patch-src-barchart.diff science/ggobi/files/patch-src-texture.diff science/gildas/files/patch-admin-gildas-env.sh.diff science/gmsh/Portfile science/gmsh/files/patch-CMakeLists.txt.diff science/gmt4/Portfile science/gnucap/Portfile science/gnucap/files/patch-Make2.g++ science/gnuradio/files/patch-cmake-expand.devel.diff science/gnuradio/files/patch-cmake-expand.release.diff science/gnuradio/files/patch-gnuradio-core_src_lib_io_ppio_ppdev.h.diff science/gnuradio/files/patch-gnuradio-core_swig_include-std_string.i.diff science/gnuradio/files/patch-gnuradio-core_swig_std_std_container.i.diff science/gnuradio/files/patch-path-order.diff science/gnuradio/files/patch-volk_gen_archs.xml.legacy.diff science/gnuradio/files/patch-volk_lib_CMakeLists.txt.legacy.diff science/gplcver/Portfile science/gplcver/files/patch-inst_tst.sh.diff science/gpp4/Portfile science/gqrx/files/patch-fix-real-imag.diff science/gqrx/files/patch-gqrx.pro-legacy.diff science/gqrx/files/patch-gqrx.pro.diff science/gr-fcdproplus/Portfile science/gr-pyqt/Portfile science/gr-rds/files/patch-lib_encoder_impl.cc.diff science/gromacs/Portfile science/gst-plugins-math/Portfile science/gstlal-calibration/Portfile science/gvemod-cplxview/Portfile science/gvemod-crayola/Portfile science/gvemod-ndview/Portfile science/gvemod-xforms-example/Portfile science/gvemodules-xforms/Portfile science/gwyddion/Portfile science/gwyddion/files/Info.plist science/h4h5tools/Portfile science/h5utils/Portfile science/hamlib/Portfile science/hdf5-lz4-plugin/Portfile science/hdfeos/Portfile science/hdfeos5/Portfile science/healpix-cxx/Portfile science/healpix/Portfile science/healpix/files/patch-build.xml.diff science/hmmer/Portfile science/htcondor/files/condor_config.local science/ifeffit/Portfile science/indi/Portfile science/jags/Portfile science/jmol/Portfile science/kst/Portfile science/kst/files/patch-CMakeLists.diff science/libANN/Portfile science/libctl/Portfile 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science/yorick-spydr/Portfile science/yorick-yao/Portfile science/yorick-yeti/Portfile science/yorick/Portfile IO error encountered -- skipping file deletion

sent 22823 bytes received 1235989 bytes 503524.80 bytes/sec total size is 41519260 speedup is 32.98 rsync error: some files could not be transferred (code 23) at /SourceCache/rsync/rsync-45/rsync/main.c(1400) [generator=2.6.9] Command failed: /usr/bin/rsync -rtzv --delete-after '--exclude=/PortIndex*' rsync://rsync.macports.org/release/ports/ /opt/local/var/macports/sources/rsync.macports.org/release/ports Exit code: 23 Error: Synchronization of the local ports tree failed doing rsync Error: Couldn't sync the ports tree: Synchronization of 1 source(s) failed To report a bug, follow the instructions in the guide:

​http://guide.macports.org/#project.tickets

Error: /opt/local/bin/port: port selfupdate failed: Couldn't sync the ports tree: Synchronization of 1 source(s) failed