Best way to upgrade installed programs

J

jonfr

What is the best way to upgrade installed programs in FreeBSD? I have been looking into this for some time now but I am not yet sure what I need to run so that I can upgrade installed programs when needed.

Thanks for the help.
 
Start here: [thread=26140]HOWTO: keeping FreeBSD's base system and packages up-to-date[/thread]
 
Thanks. I am looking into that guide now. When I was checking packages I found this issue. It seems that I have both mysql-5.5.32 and mysql-5.5.34 installed at the same time. Yet I cannot remove mysql-5.5.32. I get this error after I use make deinstall.

Code: 
root@saturn:/usr/ports/databases/mysql55-server # make install clean
===>  Installing for mysql55-server-5.5.34
===>   mysql55-server-5.5.34 depends on shared library: mysqlclient.18 - found
===>   Generating temporary packing list
===>  Checking if databases/mysql55-server already installed
===>   An older version of databases/mysql55-server is already installed (mysql-server-5.5.32)
      You may wish to ``make deinstall'' and install this port again
      by ``make reinstall'' to upgrade it properly.
      If you really wish to overwrite the old port of databases/mysql55-server
      without deleting it first, set the variable "FORCE_PKG_REGISTER"
      in your environment or the "make install" command line.
*** [check-already-installed] Error code 1

Stop in /usr/ports/databases/mysql55-server.
*** [install] Error code 1

Stop in /usr/ports/databases/mysql55-server.
 
This requires some great care.

First start by checking which ports depend on the MySQL version which you want to remove, you'll need the -R option for this: # pkg_info -R mysql-5.5.32.

If no ports depend on this you're home free; just remove it by forcing it's removal as shown above. Otherwise you need a different approach because you might risk breaking dependencies, and that is a bad thing.

In that case I'd suggest to use ports-mgmt/portmaster which can resolve this for you.

One possible complication; normally you'd use the -o parameter to tell portmaster that it needs to replace one port with the other (while making sure dependencies are met). In this case that will become a bit harder because both ports are already installed.

I guess I'd also try to force-remove the old version, then use portmaster --check-depends to get a good idea of the damage, optionally re-installing the ports which now have broken dependencies.
 
Thanks. I removed that version. But now I want to move to mysql-5.6. I have installed mysql-5.6 but mysql-5.5.33 is always pulled even if I have newer version installed.

Code: 
pkg_delete mysql-client-5.5.33
pkg_delete: package 'mysql-client-5.5.33' is required by these other packages
and may not be deinstalled:
apache24-2.4.6
apr-1.4.8.1.5.2
mysql-server-5.5.33
net-snmp-5.7.2_3
ntp-4.2.6p5_2
p5-DBD-mysql55-4.023
pecl-pdflib-2.1.10
php55-5.5.0
php55-bz2-5.5.0
php55-calendar-5.5.0
php55-ctype-5.5.0
php55-curl-5.5.0
php55-dom-5.5.0
php55-exif-5.5.0
php55-extensions-1.7
php55-fileinfo-5.5.0
php55-filter-5.5.0
php55-ftp-5.5.0
php55-gd-5.5.0
php55-gettext-5.5.0
php55-hash-5.5.0
php55-iconv-5.5.0
php55-json-5.5.0
php55-mcrypt-5.5.0
php55-mysql-5.5.0
php55-mysqli-5.5.0
php55-openssl-5.5.0
php55-pdo-5.5.0
php55-pdo_sqlite-5.5.0
php55-phar-5.5.0
php55-posix-5.5.0
php55-session-5.5.0
php55-simplexml-5.5.0
php55-snmp-5.5.0
php55-sqlite3-5.5.0
php55-tokenizer-5.5.0
php55-xml-5.5.0
php55-xmlreader-5.5.0
php55-xmlwriter-5.5.0
php55-zip-5.5.0
php55-zlib-5.5.0

I am wondering if I can use the upgrade information in this post here for this issue. It is important for me to keep the system in order so it works properly.

Thanks for the help.
 
I clearly have some issues with installed ports on my system. It's my fault, but I want to clean up any duplicates that are installed. I appear to have two versions of mrtg installed.

Code: 
pkgdb -F
--->  Checking the package registry database
[Updating the pkgdb <format:bdb_btree> in /var/db/pkg ... - 187 packages found (-1 +4) (...).... done]
Duplicated origin: net-mgmt/mrtg - mrtg-2.17.4_3,1 mrtg-2.17.4_4,1
Unregister any of them? [no] no

How do I fix this issues?

Thanks for the help.
 
In many cases, two different versions of a port will install to the same place. To fix that, both must be deinstalled (errors will be shown due to overwritten files) and then the right one alone installed.

I suggest you stop using and uninstall portupgrade and just use ports-mgmt/portmaster.
 
I did run make deinstall on portupgrade. But I got the following errors below. It was removed, but I am bit confused on what exactly is going on with my FreeBSD system. I have fixed the mysql issue. What I have not fixed is to update the packages that did use mysql-5.5. I am going to run manual updates on some of them if I can.


Code: 
root@saturn:/usr/ports/ports-mgmt/portupgrade # make deinstall
===>  Deinstalling for ports-mgmt/portupgrade
===>   Deinstalling portupgrade-2.4.11,2
pkg_delete: '/usr/local/man/man1/pkg_which.1.gz' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/man/man1/portinstall.1.gz' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/man/man1/portsvnweb.1.gz' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/man/man1/ports_glob.1.gz' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/sbin/pkg_which' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/sbin/pkgdb' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgdb.rb' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgtools.rb' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/revision.rb' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/share/zsh/site-functions/_pkgtools' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/share/examples/pkgtools/bash/complete.sample' fails original MD5 checksum - deleted anyway.
pkg_delete: '/usr/local/share/doc/pkgtools/NEWS.md' fails original MD5 checksum - deleted anyway.
===>   Deinstalling portupgrade-2.4.11.2_1,2
pkg_delete: file '/usr/local/man/man1/pkg_deinstall.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkg_fetch.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkg_glob.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkg_sort.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkg_which.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkgdb.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/pkgdu.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portcvsweb.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portinstall.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/ports_glob.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portsclean.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portsdb.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portsvnweb.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portupgrade.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man1/portversion.1.gz' doesn't exist
pkg_delete: file '/usr/local/man/man5/pkgtools.conf.5.gz' doesn't exist
pkg_delete: file '/usr/local/sbin/pkg_deinstall' doesn't exist
pkg_delete: file '/usr/local/sbin/pkg_fetch' doesn't exist
pkg_delete: file '/usr/local/sbin/pkg_glob' doesn't exist
pkg_delete: file '/usr/local/sbin/pkg_sort' doesn't exist
pkg_delete: file '/usr/local/sbin/pkg_which' doesn't exist
pkg_delete: file '/usr/local/sbin/pkgdb' doesn't exist
pkg_delete: file '/usr/local/sbin/pkgdu' doesn't exist
pkg_delete: file '/usr/local/sbin/portcvsweb' doesn't exist
pkg_delete: file '/usr/local/sbin/portsvnweb' doesn't exist
pkg_delete: file '/usr/local/sbin/portinstall' doesn't exist
pkg_delete: file '/usr/local/sbin/ports_glob' doesn't exist
pkg_delete: file '/usr/local/sbin/portsclean' doesn't exist
pkg_delete: file '/usr/local/sbin/portsdb' doesn't exist
pkg_delete: file '/usr/local/sbin/portupgrade' doesn't exist
pkg_delete: file '/usr/local/sbin/portversion' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkg.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgdb.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgdbtools.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkginfo.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgmisc.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgtools.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgtsort.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/pkgversion.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/portinfo.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/ports.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/portsdb.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools/revision.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools.rb' doesn't exist
pkg_delete: file '/usr/local/lib/ruby/site_ruby/1.9/pkgtools' doesn't exist
pkg_delete: unable to completely remove directory '/usr/local/lib/ruby/site_ruby/1.9/pkgtools'
pkg_delete: file '/usr/local/etc/pkgtools.conf.sample' doesn't exist
pkg_delete: file '/usr/local/etc/pkgtools.status-pkg.sh' doesn't exist
pkg_delete: file '/usr/local/share/zsh/site-functions/_pkgtools' doesn't exist
pkg_delete: file '/usr/local/share/examples/pkgtools/bash/complete.sample' doesn't exist
pkg_delete: file '/usr/local/share/examples/pkgtools/tcsh/complete.sample' doesn't exist
pkg_delete: file '/usr/local/share/doc/pkgtools/NEWS.md' doesn't exist
pkg_delete: file '/usr/local/share/doc/pkgtools/README.md' doesn't exist
pkg_delete: file '/usr/local/share/examples/pkgtools/bash' doesn't exist
pkg_delete: unable to completely remove directory '/usr/local/share/examples/pkgtools/bash'
pkg_delete: file '/usr/local/share/examples/pkgtools/tcsh' doesn't exist
pkg_delete: unable to completely remove directory '/usr/local/share/examples/pkgtools/tcsh'
pkg_delete: file '/usr/local/share/examples/pkgtools' doesn't exist
pkg_delete: unable to completely remove directory '/usr/local/share/examples/pkgtools'
pkg_delete: file '/usr/local/share/doc/pkgtools' doesn't exist
pkg_delete: unable to completely remove directory '/usr/local/share/doc/pkgtools'
pkg_delete: file '/usr/local/libdata/ldconfig/portupgrade' doesn't exist
pkg_delete: couldn't entirely delete package `portupgrade-2.4.11.2_1,2'
(perhaps the packing list is incorrectly specified?)
 
For some reason mysql-5.5.34 is no longer being pulled into the package system. I still have to update the remaining packages and keep my system in order and I have not yet found out how to update many package with single command. If that is even possible.
 
I was following the this information /usr/ports/UPDATING and I did run portmaster -r perl. When I got to the end, I got this information.

Code: 
===>>> The following actions will be taken if you choose to proceed:
        Upgrade perl-threaded-5.14.4 to perl-5.14.4_2
        Re-install isc-dhcp42-server-4.2.5
        Re-install p5-Locale-gettext-1.05_3
        Upgrade gettext-0.18.3 to gettext-0.18.3.1
        Re-install help2man-1.43.3
        Re-install autoconf-2.69
        Upgrade m4-1.4.16_1,1 to m4-1.4.17,1
        Re-install automake-1.14
        Re-install mrtg-2.17.4_4,1
        Upgrade gd-2.0.35_9,1 to libgd-2.1.0_1,1
        Install graphics/tiff
        Upgrade libtool-2.4.2_1 to libtool-2.4.2_2
        Install graphics/jbigkit
        Upgrade freetype2-2.4.12_1 to freetype2-2.5.0.1
        Upgrade fontconfig-2.9.0,1 to fontconfig-2.10.95,1
        Upgrade libX11-1.6.0,1 to libX11-1.6.2,1
        Upgrade xorg-macros-1.17 to xorg-macros-1.17.1
        Upgrade libXpm-3.5.10 to libXpm-3.5.11
        Re-install p5-Net-SNMP-6.0.1
        Re-install p5-Crypt-DES-2.07
        Re-install p5-Crypt-CBC-2.33
        Re-install p5-Digest-HMAC-1.03
        Re-install p5-Digest-SHA1-2.13
        Re-install p5-SNMP_Session-1.13_2
        Re-install p5-IO-Socket-INET6-2.69
        Re-install p5-Socket6-0.23
        Upgrade mrtg-2.17.4_3,1 to mrtg-2.17.4_4,1
        Re-install net-snmp-5.7.2_3
        Install lang/python
        Install lang/python2
        Upgrade python27-2.7.5_1 to python27-2.7.5_3
        Re-install p5-Net-SSLeay-1.55
        Re-install p5-IO-Tty-1.10
        Re-install p5-Authen-PAM-0.16_1
        Upgrade webmin-1.630 to webmin-1.660
        Re-install p5-Mozilla-CA-20130114
        Re-install ntp-4.2.6p5_2
        Upgrade php55-5.5.0 to php55-5.5.5
        Re-install apache24-2.4.6
        Upgrade php55-bz2-5.5.0 to php55-bz2-5.5.5
        Upgrade php55-calendar-5.5.0 to php55-calendar-5.5.5
        Upgrade php55-ctype-5.5.0 to php55-ctype-5.5.5
        Upgrade php55-curl-5.5.0 to php55-curl-5.5.5
        Upgrade curl-7.24.0_3 to curl-7.32.0
        Upgrade libidn-1.27 to libidn-1.28_1
        Install multimedia/rtmpdump
        Install security/libssh2
        Upgrade php55-dom-5.5.0 to php55-dom-5.5.5
        Upgrade php55-exif-5.5.0 to php55-exif-5.5.5
        Upgrade php55-fileinfo-5.5.0 to php55-fileinfo-5.5.5
        Upgrade php55-filter-5.5.0 to php55-filter-5.5.5
        Upgrade php55-ftp-5.5.0 to php55-ftp-5.5.5
        Upgrade php55-gd-5.5.0 to php55-gd-5.5.5
        Upgrade php55-gettext-5.5.0 to php55-gettext-5.5.5
        Upgrade php55-hash-5.5.0 to php55-hash-5.5.5
        Upgrade php55-iconv-5.5.0 to php55-iconv-5.5.5
        Upgrade php55-json-5.5.0 to php55-json-5.5.5
        Upgrade php55-mcrypt-5.5.0 to php55-mcrypt-5.5.5
        Upgrade libltdl-2.4.2_1 to libltdl-2.4.2_2
        Upgrade php55-mysql-5.5.0 to php55-mysql-5.5.5
        Upgrade php55-mysqli-5.5.0 to php55-mysqli-5.5.5
        Upgrade php55-openssl-5.5.0 to php55-openssl-5.5.5
        Re-install pdflib-7.0.5_2
        Re-install pecl-pdflib-2.1.10
        Upgrade php55-pdo-5.5.0 to php55-pdo-5.5.5
        Upgrade php55-pdo_sqlite-5.5.0 to php55-pdo_sqlite-5.5.5
        Upgrade php55-phar-5.5.0 to php55-phar-5.5.5
        Upgrade php55-posix-5.5.0 to php55-posix-5.5.5
        Upgrade php55-session-5.5.0 to php55-session-5.5.5
        Upgrade php55-simplexml-5.5.0 to php55-simplexml-5.5.5
        Upgrade php55-snmp-5.5.0 to php55-snmp-5.5.5
        Upgrade php55-sqlite3-5.5.0 to php55-sqlite3-5.5.5
        Upgrade php55-tokenizer-5.5.0 to php55-tokenizer-5.5.5
        Upgrade php55-xml-5.5.0 to php55-xml-5.5.5
        Upgrade php55-xmlreader-5.5.0 to php55-xmlreader-5.5.5
        Upgrade php55-xmlwriter-5.5.0 to php55-xmlwriter-5.5.5
        Upgrade php55-zip-5.5.0 to php55-zip-5.5.5
        Upgrade php55-zlib-5.5.0 to php55-zlib-5.5.5
        Upgrade php55-extensions-1.7 to php55-extensions-1.8
        Install databases/php55-pgsql
        Install databases/postgresql90-client
        Install mail/php55-imap
        Install mail/cclient
        Install www/php55-opcache
        Re-install p5-Net-Daemon-0.48
        Re-install p5-PlRPC-0.2020_1
        Re-install p5-DBI-1.628
        Re-install p5-URI-1.60
        Re-install p5-ExtUtils-Constant-0.23
        Re-install p5-Socket-2.012
        Re-install p5-IO-Socket-IP-0.24
        Re-install p5-IO-Socket-SSL-1.953
        Re-install p5-Net-HTTP-6.06
        Re-install p5-LWP-Protocol-https-6.04
        Re-install p5-Crypt-SSLeay-0.64
        Re-install mysql56-server-5.6.14
        Upgrade p5-DBD-mysql55-4.023 to p5-DBD-mysql55-4.024
        Install databases/mysql55-client

===>>> Proceed? y/n [y] n

This still wants to install databases/mysql55-client even if I have databases/mysql56-client installed. From the looks of this, I think I am stuck with mysql-5.5 for a while longer.
 
Thanks. I am trying to find the portmaster command so that I can update the rest of installed packages.

I am also updating other server that I do not own and I see this error in when I run pkg_version -v | grep -v up-to-date . I am not sure how to correct it or fix it.

Code: 
gio-fam-backend-2.34.3              !   Comparison failed

Thanks for the help.
 
jonfr said:
I am also updating other server that I do not own and I see this error in when I run pkg_version -v | grep -v up-to-date .
Click to expand...
You can do this in one go: pkg_version -vL'='

I am not sure how to correct it or fix it.

Code: 
gio-fam-backend-2.34.3              !   Comparison failed

Thanks for the help.
Click to expand...

Read /usr/ports/UPDATING:
Code: 
20130731:
  AFFECTS: users of glib20
  AUTHOR: kwm@FreeBSD.org

  The devel/gio-fam-backend port was removed in the glib 2.36 update.
  Since the gio-fam-backend port was used in USE_GNOME=glib20, all
  dependencies need to be rebuilt. The removal of gio-fam-backend isn't
  critical, glib20 using programs should work just fine if the port is still
  installed. It is not clear however, if glib20 will use the new kqueue
  backend or the old fam backend.

  Note that users of pkg packages can just run the pkg delete command after
  their next update.

  # portmaster -r gio-fam-backend
  # pkg_delete gio-fam-backend-\* (for pkgng: pkg delete gio-fam-backend)
  # portmaster -a

  or

  # portupgrade -rf gio-fam-backend
  # pkg_delete gio-fam-backend-\* (for pkgng: pkg delete gio-fam-backend)
  # portupgrade -a
 
Thanks. When I run it on my own server I get this.

Code: 
pkg_version -vL'='
alsa-lib-1.0.26                     <   needs updating (port has 1.0.27.2)
bootstrap-openjdk-r316538           <   needs updating (port has r330538)
bsdadminscripts-6.1.1_1             <   needs updating (port has 6.1.1_4)
cmake-modules-2.8.11.2              <   needs updating (port has 2.8.11.2_1)
compat8x-amd64-8.4.804000.201309_1  <   needs updating (port has 8.4.804000.201310_1)
gmp-5.1.2                           <   needs updating (port has 5.1.3)
java-zoneinfo-2013.d                <   needs updating (port has 2013.g)
libSM-1.2.1,1                       <   needs updating (port has 1.2.2,1)
libXaw-1.0.11,2                     <   needs updating (port has 1.0.12,2)
libXi-1.7.1_1,1                     <   needs updating (port has 1.7.2,1)
libXmu-1.1.1,1                      <   needs updating (port has 1.1.2,1)
libgcrypt-1.5.2                     <   needs updating (port has 1.5.3)
libpthread-stubs-0.3_3              <   needs updating (port has 0.3_4)
portaudit-0.6.0                     <   needs updating (port has 0.6.1)
portmaster-3.17.1                   <   needs updating (port has 3.17.2)
samba36-3.6.16                      <   needs updating (port has 3.6.18)
tdb-1.2.11,1                        <   needs updating (port has 1.2.12,1)

I am not sure what command I need to run to update all this programs in one go. If that is possible to start with.

When I run it on the server (that I do not own) I am now updating and fixing I get this errors. I think the owner has been 'working' on it on his own and that is creating this issues from the looks of it. I have strict update process on my own server to prevent this type of problems.

See attachment.

Here are problem that I am not sure how to fix. I also need to track down and remove php5-mssql. It is not used.

Thanks for the help.
 

Attachments

Start by reading /usr/ports/UPDATING. Sometimes ports need to be updated in a specific order (or disappear completely, like your gio-fam-backend). If none of it applies you can do a portmaster -a to upgrade all ports.

Remove whatever you don't use or need before updating. You can remove them with pkg_delete(1).
 
I was running # portmaster --check-depends in order to check for errors due to a mistake that I made. I got this in that check. I am not sure what to do.

Code: 
===>>> Checking php5-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-bz2-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-ctype-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-curl-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-dom-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-exif-5.4.13
        ===>>> Updating @pkgdep for www/apache24
        ===>>> Installing the new +CONTENTS file
===>>> Checking php5-extensions-1.7
        ===>>> Updating @pkgdep for net-mgmt/net-snmp

        ===>>> net-mgmt/php5-snmp is listed as a dependency
        ===>>> but there is no installed version

        ===>>> Delete this dependency data? y/n [n] n
[...]


===>>> lang/php53 is listed as a dependency
        ===>>> but there is no installed version

        ===>>> Delete this dependency data? y/n [n] n

        ===>>> Installing the new +CONTENTS file
===>>> Checking php53-ctype-5.3.23
        ===>>> Updating @pkgdep for www/apache24

        ===>>> lang/php53 is listed as a dependency
        ===>>> but there is no installed version

        ===>>> Delete this dependency data? y/n [n] n

[...]

Thanks for the help.
 
"Update all these programs in one go". Difficult, but I do the following with restarts...
Code: 
cat ports.list.problems.txt | grep -v php | awk '{print $1}' | xargs -J % portmaster -d -B -P -i -g -x gcc-4.7.3.2013.0323 --update-if-newer %
( I only put the php in there as an example, you can update those after all the rest are done maybe... ). Maybe test it on one or two ports first if you know the command pipe syntax already.
 
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