Problem syncing MacPorts

[ClintO (Clint O)]

I've been using MacPorts for ages and have never seen an error like this before:

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

sent 36 bytes  received 30250 bytes  20190.67 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/kde/kde-l10n-eu/files/patch-CMakeLists.txt.diff" (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/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
IO error encountered -- skipping file deletion

sent 53 bytes  received 819686 bytes  546492.67 bytes/sec
total size is 41246975  speedup is 50.32
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

I attempted to look at one of the files it complained about, and I don't see anything immediately wrong:

poly /opt/local/var/macports/sources/rsync.macports.org/release$ ll ports/science/viking/files/autogen.sh
-rw-r--r--  1 root  admin  1194 Apr 29 00:30 ports/science/viking/files/autogen.sh

[ryandesign (Ryan Carsten Schmidt)]

Duplicate of #49233.