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-RULES__rules.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-Pantomime__Upgraded_.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-lib__xstrrpl.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-lsb__lsbhreader.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
science/libframe/Portfile
science/libnc-dap/Portfile
science/libnova/Portfile
science/liboglappth/Portfile
science/libstree/files/create-dylib.sh
science/libstree/files/patch-src__lst_string.h
science/libtcd/Portfile
science/libxc/Portfile
science/liquid-dsp/files/patch-makefile.in.diff
science/liquid-dsp/files/patch-src_modem_src_freqmod.c.diff
science/magic-devel/Portfile
science/maniview/files/patch-maniview.c.diff
science/mddisplay/Portfile
science/minc/Portfile
science/miriad/Portfile
science/mmdb/Portfile
science/ncarg/files/patch-config-ymake.diff
science/ncview/Portfile
science/ncview/files/patch-configure.diff
science/ndmanager2/Portfile
science/ocaml-mpi/files/Makefile.diff
science/ompl/Portfile
science/openbabel/Portfile
science/openbabel/files/patch-shared_ptr.diff
science/opendx/files/configure.ac.diff
science/opendx/files/main.diff
science/opendx/files/patch-src-exec-dpexec-packet.c.diff
science/openmpi/files/openmpi-devel-gcc43-fortran
science/openscad/Portfile
science/pdb2pqr/Portfile
science/peekabot-client/files/patch-disable_compression.diff
science/perlprimer/Portfile
science/plplot510/files/patch-plConfig.h.in.diff
science/pqp/files/patch-src-PQP_Compile.h.diff
science/pvm/Portfile
science/pymol/files/pmg_tk_platform.patch
science/pymol/files/pymol_shell.diff
science/qfsm/Portfile
science/qucs/Portfile
science/qucs/files/patch-configure.diff
science/relax/files/relax.patch
science/root/Portfile
science/root5/files/patch-builtin-afterimage-disabletiff.diff
science/root5/files/root5
science/sbsat/files/patch-configure.ac.diff
science/sbsat/files/patch-src-generator-Makefile.am.diff
science/sbsat/files/patch-src-generator-gentest.cc.diff
science/sbsat/files/slider3_base.py
science/scidavis/files/patch-OriginObj.diff
science/scidavis/files/patch-noQtAssistant.diff
science/scotch/Portfile
science/seqan-apps/Portfile
science/setiathome/Portfile
science/setiathome/files/patch-README.diff
science/skymaker/Portfile
science/solid/Portfile
science/solid/files/patch-GLUT.diff
science/solid/files/patch-configure.ac.diff
science/sparky/Portfile
science/sparky/files/sparky-build.diff
science/stiff/Portfile
science/tempo/files/patch-tempo.c.diff
science/tophat/Portfile
science/triangle/Portfile
science/vbs/Portfile
science/vbs/files/patch-Makefile.in
science/viking/Portfile
science/wcalc/files/patch-utils_shtml2html.diff
science/weka/files/patch-build.xml.diff
science/whizard/Portfile
science/xastir/files/patch-configure.ac.diff
science/xephem/files/patch-Makefile.diff
science/xloops/files/patch-fcntimer.cpp
science/xloops/files/patch-ginsh_parser.yy
science/xpa/Portfile
science/xraylib/files/configure.ac.diff
science/xrmc/Portfile
science/xrootd/files/patch-cmake-XRootDOSDefs.cmake.diff
science/yorick-av/Portfile
science/yorick-cubeview/Portfile
science/yorick-imutil/Portfile
science/yorick-ml4/Portfile
science/yorick-ml4/files/patch-ml4.i.diff
science/yorick-soy/Portfile
science/yorick-soy/files/patch-soy.i.diff
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

[ryandesign (Ryan Carsten Schmidt)]

Duplicate of #49233.