Installing fresh MacPorts

[Rodolfo Aramayo]

Ryan,

To make a long story short. I am installing a fresh installation of
MacPorts on a fresh installation of the MacOSX10.6 system software

I am running into a series of issues. Some of them really creepy and
that I will address later on another email. The more benign issues I
am consistently running into and that I cannot resolve are:

==========<THIS ONE IS NASTY AS IT CRASHES THE COMPUTERS BAD
--->  Computing dependencies for atlas
--->  Building atlas
Error: Target org.macports.build returned: shell command failed (see
log for details)
Log for atlas is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>
==========
26# tail -50 /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
:info:build
:info:build       BEGIN STAGE 4-3-2: sLAPACK TUNING at 00:28
:info:build make -f Makefile ILATune pre=d 2>&1 | ./xatlas_tee
INSTALL_LOG/dLATUNE.LOG
:info:build       DONE  STAGE 4-3-2 at 00:28
:info:build
:info:build
:info:build       BEGIN STAGE 4-3-3: zLAPACK TUNING at 00:28
:info:build make -f Makefile ILATune pre=s 2>&1 | ./xatlas_tee
INSTALL_LOG/sLATUNE.LOG
:info:build       DONE  STAGE 4-3-3 at 00:28
:info:build
:info:build
:info:build       BEGIN STAGE 4-3-4: cLAPACK TUNING at 00:28
:info:build make -f Makefile ILATune pre=z 2>&1 | ./xatlas_tee
INSTALL_LOG/zLATUNE.LOG
:info:build       DONE  STAGE 4-3-4 at 00:28
:info:build    DONE  STAGE 4-3-0 at 00:28
:info:build DONE  STAGE 4-0-0 at 00:28
:info:build
:info:build
:info:build BEGIN STAGE 5-0-0: FINAL LIBRARY UPDATE at 00:28
:info:build
:info:build
:info:build    BEGIN STAGE 5-1-0: FINAL STATIC LIBRARY UPDATE at 00:28
:info:build make -f Makefile IBuildLibs IBuildPtlibs0 2>&1 |
./xatlas_tee INSTALL_LOG/LIBUPDATE.LOG
:info:build    DONE  STAGE 5-1-0 at 00:28
:info:build
:info:build
:info:build
:info:build
:info:build ATLAS install complete.  Examine
:info:build ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details.
:info:build make[1]: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.9.47/build'
:info:build /usr/bin/make clean
:info:build make[1]: Entering directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.9.47/build'
:info:build rm -rf *.dSYM
:info:build rm -rf *.o x* config?.out *core*
:info:build make[1]: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.9.47/build'
:info:build make: Leaving directory
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.9.47/build'
:debug:build Executing proc-post-org.macports.build-build-0
:info:build ld: duplicate symbol _ATL_SetAtomicCount in
libatlas.a(ATL_SetAtomicCount_mut.o) and
libatlas.a(ATL_SetAtomicCount_arch.o)
:info:build shell command "cd
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/atlas-3.9.47/build/lib
&&  ( test ! -e libatlas.a ||  /usr/bin/ld -arch x86_64 -dynamic
-dylib -single_module -dead_strip  -x -all_load -L.
-L/opt/local/lib/gcc44/x86_64  -L/opt/local/lib/gcc44 -ldylib1.o
-dylib_install_name /opt/local/lib/libatlas.dylib  libatlas.a -o
libatlas.dylib  -lSystem  )" returned error 1
:error:build Target org.macports.build returned: shell command failed
(see log for details)
:debug:build Backtrace: shell command failed (see log for details)
    while executing
"$post $targetname"
:info:build Warning: the following items did not execute (for atlas):
org.macports.activate org.macports.build org.macports.destroot
org.macports.install
:error:build Failed to install atlas
: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 Log for atlas is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
==========



==========
--->  Attempting to fetch openssl-1.0.0d_0.darwin_10.x86_64.tbz2 from
http://packages.macports.org/openssl
--->  Attempting to fetch
openssl-1.0.0d_0.darwin_10.x86_64.tbz2.rmd160 from
http://packages.macports.org/openssl
--->  Installing openssl @1.0.0d_0
--->  Deactivating openssl @1.0.0d_0+universal
Error: Target org.macports.deactivate returned: could not read
"/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
Log for openssl is at:
/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0+universal/openssl/main.log
Warning: Failed to execute portfile from registry for openssl
@1.0.0d_0+universal
==========
60# tail -50 /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0+universal/openssl/main.log
:debug:deactivate deactivating link:
/opt/local/share/man/man3/CMS_ReceiptRequest_create0.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_strdup.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_new.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_grow.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_free.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_zero.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_value_one.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_ucmp.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_to_montgomery.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_swap.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_sub_word.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_sub.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_sqr.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_set_word.3ssl.gz
:debug:deactivate deactivating file:
/opt/local/share/man/man3/BN_set_bit.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_rshift1.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_rshift.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_rand.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_pseudo_rand.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_print_fp.3ssl.gz
:error:deactivate Target org.macports.deactivate returned: could not
read "/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
:debug:deactivate Backtrace: could not read
"/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
    while executing
"file type $dstfile"
    (procedure "_deactivate_file" line 2)
    invoked from within
"_deactivate_file $file"
    ("foreach" body line 2)
    invoked from within
"foreach file $files {
                _deactivate_file $file
            }"
    invoked from within
"registry::write {
            $port deactivate $imagefiles
            foreach file $files {
                _deactivate_file $file
            }
    ..."
    (procedure "_deactivate_contents" line 37)
    invoked from within
"_deactivate_contents $requested [$requested files] $force"
    (procedure "portimage::deactivate" line 54)
    invoked from within
"registry_deactivate $subport $version $revision $portvariants [array
get user_options]"
    (procedure "portdeactivate::deactivate_main" line 3)
    invoked from within
"$procedure $targetname"
:info:deactivate Warning: the following items did not execute (for
openssl): org.macports.deactivate
:notice:deactivate Log for openssl is at:
/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0+universal/openssl/main.log
==========


==========
--->  Computing dependencies for texlive-latex-extra
--->  Cleaning texlive-latex-extra
--->  Computing dependencies for texlive-latex-recommended
--->  Cleaning texlive-latex-recommended
--->  Configuring texlive-latex3
Error: texlive-latex3 has been replaced by texlive-latex-recommended;
please install that port instead
Error: Target org.macports.configure returned: obsolete port
Log for texlive-latex3 is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_tex_texlive-latex3/texlive-latex3/main.log
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>
==========
62# tail -50  /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_tex_texlive-latex3/texlive-latex3/main.log
version:1
:debug:main Executing org.macports.main (texlive-latex3)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:main Skipping completed org.macports.archivefetch (texlive-latex3)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (texlive-latex3)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (texlive-latex3)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (texlive-latex3)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (texlive-latex3)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Mon Sep  5 00:21:33 CDT 2011
:notice:configure --->  Configuring texlive-latex3
:debug:configure Using compiler 'Mac OS X gcc 4.2'
:debug:configure Executing proc-pre-org.macports.configure-configure-0
:error:configure texlive-latex3 has been replaced by
texlive-latex-recommended; please install that port instead
:error:configure Target org.macports.configure returned: obsolete port
:debug:configure Backtrace: obsolete port
    while executing
"$pre $targetname"
:info:configure Warning: the following items did not execute (for
texlive-latex3): org.macports.activate org.macports.configure
org.macports.build org.macports.destroot org.macports.install
:notice:configure Log for texlive-latex3 is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_tex_texlive-latex3/texlive-latex3/main.log
==========

==========
--->  Cleaning gdbm
--->  Activating gdbm @1.9.1_0+universal
--->  Cleaning gdbm
--->  Deactivating openssl @1.0.0d_0
Error: Target org.macports.deactivate returned: could not read
"/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
Log for openssl is at:
/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0/openssl/main.log
Warning: Failed to execute portfile from registry for openssl @1.0.0d_0
==========
64# tail -50 /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0/openssl/main.log
:debug:deactivate deactivating link:
/opt/local/share/man/man3/CMS_ReceiptRequest_create0.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_strdup.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_new.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_grow.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BUF_MEM_free.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_zero.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_value_one.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_ucmp.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_to_montgomery.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_swap.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_sub_word.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_sub.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_sqr.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_set_word.3ssl.gz
:debug:deactivate deactivating file:
/opt/local/share/man/man3/BN_set_bit.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_rshift1.3ssl.gz
:debug:deactivate deactivating link: /opt/local/share/man/man3/BN_rshift.3ssl.gz
:debug:deactivate deactivating file: /opt/local/share/man/man3/BN_rand.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_pseudo_rand.3ssl.gz
:debug:deactivate deactivating link:
/opt/local/share/man/man3/BN_print_fp.3ssl.gz
:error:deactivate Target org.macports.deactivate returned: could not
read "/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
:debug:deactivate Backtrace: could not read
"/opt/local/share/man/man3/BN_print.3ssl.gz": no such file or
directory
    while executing
"file type $dstfile"
    (procedure "_deactivate_file" line 2)
    invoked from within
"_deactivate_file $file"
    ("foreach" body line 2)
    invoked from within
"foreach file $files {
                _deactivate_file $file
            }"
    invoked from within
"registry::write {
            $port deactivate $imagefiles
            foreach file $files {
                _deactivate_file $file
            }
    ..."
    (procedure "_deactivate_contents" line 37)
    invoked from within
"_deactivate_contents $requested [$requested files] $force"
    (procedure "portimage::deactivate" line 54)
    invoked from within
"registry_deactivate $subport $version $revision $portvariants [array
get user_options]"
    (procedure "portdeactivate::deactivate_main" line 3)
    invoked from within
"$procedure $targetname"
:info:deactivate Warning: the following items did not execute (for
openssl): org.macports.deactivate
:notice:deactivate Log for openssl is at:
/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_openssl_1.0.0d_0/openssl/main.log
==========

Help will be appreciated

Thanks

--R