xcrun: error: unable to exec Xcode native xcrun (Permission denied).

[mr.nice_365@…]

seems like that happened before and some said that's not the reason for what's going wrong but after upgrading to Mavericks none of the ports I tried to install worked (bzip2, openssl, cmake), all with the same error.

I followed all steps of Migration and even ​http://guide.macports.org/chunked/installing.macports.uninstalling.html

One Problem I run into when following the Migration guide was when installing the Command Line Tools via xcode-select --install "Can't install ... because ... not available... from ... Software Update server." Therefore I downloaded the Command Line Tools for Mavericks manually

here's the error I get when trying to install any port (tclIndex is in the Scripts subfolder)

cat /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/main.log
version:1
:debug:main Attempting ln -sf /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2/work
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 503
:debug:main Executing org.macports.main (bzip2)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:archivefetch archivefetch phase started at Sat Nov  2 20:12:14 CET 2013
:msg:archivefetch --->  Fetching archive for bzip2
:debug:archivefetch Executing org.macports.archivefetch (bzip2)
:debug:archivefetch Can't run archivefetch on this port without elevated privileges. Escalating privileges back to root.
:debug:archivefetch euid changed to: 0. egid changed to: 0.
:debug:archivefetch changing euid/egid - current euid: 0 - current egid: 0
:debug:archivefetch egid changed to: 501
:debug:archivefetch euid changed to: 503
:info:archivefetch --->  bzip2-1.0.6_0.darwin_13.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
:msg:archivefetch --->  Attempting to fetch bzip2-1.0.6_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/bzip2
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:msg:archivefetch --->  Attempting to fetch bzip2-1.0.6_0.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/bzip2
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:msg:archivefetch --->  Attempting to fetch bzip2-1.0.6_0.darwin_13.x86_64.tbz2 from http://packages.macports.org/bzip2
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
:debug:archivefetch Privilege de-escalation not attempted as not running as root.
:debug:fetch fetch phase started at Sat Nov  2 20:12:18 CET 2013
:notice:fetch --->  Fetching distfiles for bzip2
:debug:fetch Can't run fetch on this port without elevated privileges. Escalating privileges back to root.
:debug:fetch euid changed to: 0. egid changed to: 0.
:debug:fetch changing euid/egid - current euid: 0 - current egid: 0
:debug:fetch egid changed to: 501
:debug:fetch euid changed to: 503
:debug:fetch Executing org.macports.fetch (bzip2)
:info:fetch --->  bzip2-1.0.6.tar.gz doesn't seem to exist in /opt/local/var/macports/distfiles/bzip2
:notice:fetch --->  Attempting to fetch bzip2-1.0.6.tar.gz from http://lil.fr.distfiles.macports.org/bzip2
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Sat Nov  2 20:12:21 CET 2013
:notice:checksum --->  Verifying checksums for bzip2
:debug:checksum Executing org.macports.checksum (bzip2)
:info:checksum --->  Checksumming bzip2-1.0.6.tar.gz
:debug:checksum Correct (md5) checksum for bzip2-1.0.6.tar.gz
:debug:checksum Correct (sha1) checksum for bzip2-1.0.6.tar.gz
:debug:checksum Correct (rmd160) checksum for bzip2-1.0.6.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Sat Nov  2 20:12:21 CET 2013
:notice:extract --->  Extracting bzip2
:debug:extract Executing org.macports.extract (bzip2)
:info:extract --->  Extracting bzip2-1.0.6.tar.gz
:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/bzip2/bzip2-1.0.6.tar.gz'
:debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/bzip2/bzip2-1.0.6.tar.gz' | /usr/bin/tar -xf -'
:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/bzip2/bzip2-1.0.6.tar.gz' | /usr/bin/tar -xf - 
:debug:extract euid/egid changed to: 0/0
:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work to macports
:debug:extract euid/egid changed to: 503/501
:debug:extract Privilege de-escalation not attempted as not running as root.
:debug:patch patch phase started at Sat Nov  2 20:12:21 CET 2013
:debug:patch Executing org.macports.patch (bzip2)
:notice:patch --->  Applying patches to bzip2
:info:patch --->  Applying patch-Makefile-man.diff
:debug:patch Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:patch Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0'
:debug:patch Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2/files/patch-Makefile-man.diff'
:info:patch patching file Makefile
:info:patch --->  Applying patch-Makefile-links.diff
:debug:patch Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:patch Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0'
:debug:patch Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2/files/patch-Makefile-links.diff'
:info:patch patching file Makefile
:info:patch --->  Applying patch-Makefile-dylib.diff
:debug:patch Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:patch Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0'
:debug:patch Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2/files/patch-Makefile-dylib.diff'
:info:patch patching file Makefile
:debug:patch Executing proc-post-org.macports.patch-patch-0
:debug:patch Executing reinplace: /usr/bin/sed s|__MacPorts_Version__|1.0.6|g < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile >@ file12
:debug:patch euid/egid changed to: 0/0
:debug:patch chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile to macports
:debug:patch euid/egid changed to: 503/501
:debug:patch euid/egid changed to: 0/0
:debug:patch setting attributes on /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile
:debug:patch euid/egid changed to: 503/501
:debug:patch Executing reinplace: /usr/bin/sed s|__MacPorts_Compatibility_Version__|1.0|g < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile >@ file12
:debug:patch euid/egid changed to: 0/0
:debug:patch chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile to macports
:debug:patch euid/egid changed to: 503/501
:debug:patch euid/egid changed to: 0/0
:debug:patch setting attributes on /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6/Makefile
:debug:patch euid/egid changed to: 503/501
:debug:patch Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Sat Nov  2 20:12:21 CET 2013
:notice:configure --->  Configuring bzip2
:debug:configure Using compiler 'Xcode Clang'
:debug:configure Executing org.macports.configure (bzip2)
:debug:configure Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Sat Nov  2 20:12:21 CET 2013
:notice:build --->  Building bzip2
:debug:build Executing org.macports.build (bzip2)
:debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/make -j4 -w all CC="/usr/bin/clang -arch x86_64" PREFIX=/opt/local'
:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/make -j4 -w all CC="/usr/bin/clang -arch x86_64" PREFIX=/opt/local 
:info:build xcrun: error: unable to exec Xcode native xcrun (Permission denied).
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/work/bzip2-1.0.6" && /usr/bin/make -j4 -w all CC="/usr/bin/clang -arch x86_64" PREFIX=/opt/local 
:info:build Exit code: 1
:error:build org.macports.build for port bzip2 returned: command execution failed
:debug:build Error code: CHILDSTATUS 18689 1
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"$procedure $targetname"
:info:build Warning: targets not executed for bzip2: org.macports.activate org.macports.build org.macports.destroot org.macports.install
:error:build Failed to install bzip2
:debug:build couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory
    while executing
"open [file join $dir tclIndex]"
:notice:build Please see the log file for port bzip2 for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_archivers_bzip2/bzip2/main.log

[ryandesign (Ryan Carsten Schmidt)]

What you've read before is correct: an error about tclIndex is irrelevant. See #37231.

The reason your bzip2 build is failing, according to your above log, is:

xcrun: error: unable to exec Xcode native xcrun (Permission denied).

So, why is that? What happens when you manually run xcrun?

[mr.nice_365@…]

good question. xcrun works as expected but I've found out via

xcrun --show-sdk-path

that it used the wrong Xcode (had too many developer preview versions around)

I did a

xcode-select --reset

and now everything works fine again! thanks.

[98B]

What happened in my case (same error message) turned out to be due to the location of Xcode and the permissions that the location entails: the edition I had xcode-selected is installed in ~/Applications. This directory, by default, has permissions set to drwx------. Which is not good enough for user MacPorts:

$ sudo -u macports /bin/bash
bash-3.2$ xcrun
xcrun: error: unable to exec Xcode native xcrun (Permission denied).

(Some port operations seem to be carried out by this user.) I added the user MacPorts to the list of users of ~/Applications via Finder's info dialog ⌘-I, granting Read permissions, and then everything started to work as expected. (The permissions of ~/Applications look like drwx------+ now.)