Filesystem errors when installing ports

[raramayo (Rodolfo Aramayo)]

Installing Inkscape is consistently failing. I have completely deleted my MacPorts Installation and started fresh, yet I get the following error:

--->  Building boost
error reading "file12": no such device or address
Log for boost is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_devel_boost/main.log
Error: The following dependencies failed to build: boost gnome-vfs desktop-file-utils gconf dbus-glib dbus gtk-doc docbook-xml docbook-xml-4.1.2 xmlcatmgr docbook-xml-4.2 docbook-xml-4.3 docbook-xml-4.4 docbook-xml-4.5 docbook-xml-5.0 docbook-xsl gnome-doc-utils intltool gnome-common p5-getopt-long p5-pathtools p5-scalar-list-utils p5-xml-parser iso-codes libxslt py26-libxml2 rarian getopt gtk2 atk shared-mime-info xorg-libXcomposite xorg-compositeproto xorg-libXfixes xorg-fixesproto xorg-libXcursor xorg-libXdamage xorg-damageproto xorg-libXi xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto orbit2 libidl policykit eggdbus gnome-mime-data gsl gtkmm cairomm libsigcxx2 glibmm pangomm gtkspell2 enchant aspell hunspell libwpg libwpd libgsf libbonobo poppler openjpeg poppler-data py26-lxml py26-distribute py26-numpy atlas gcc44 gmp mpfr fftw-3 py26-nose py26-xml
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>

Then when I try to repeat the command I get the following and the computer crashes completely:

genomics08:~ raramayo$ sudo port install Inkscape
sudo: can't stat /etc/sudoers: Device not configured

After this I lose control of the machine via terminal. Commands like "sudo su" or "who" do not work anymore. The messages I get are like this one:

"bash: /usr/bin/who: Operation not permitted"

and the only way to re-gain control is to reboot the machine

[raramayo (Rodolfo Aramayo)]

I should add, I am installing on three machines at the same time. One machine crashed while processing Boost. Another, passed that stage and crashed at a different stage:

Error: Target org.macports.destroot returned: shell command failed
Log for gtk2 is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_x11_gtk2/main.log
Error: The following dependencies failed to build: gnome-vfs gconf gtk2 orbit2 libidl policykit eggdbus gnome-mime-data gsl gtkmm cairomm libsigcxx2 glibmm pangomm gtkspell2 enchant aspell hunspell libwpg libwpd libgsf libbonobo poppler openjpeg poppler-data py26-lxml py26-distribute py26-numpy atlas gcc44 gmp mpfr fftw-3 py26-nose py26-xml
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>

While the third machine went on undisturbed...

After rebooting the machines that crashed, I re-run the Inkscape installation command and installation seems to finish successfully...

Can any one explain what is happening?

Thanks Guys. Thanks

[ryandesign (Ryan Carsten Schmidt)]

Please use WikiFormatting so your posts are legible.

You have something extremely strange going on with your machine, but I have no idea what it is. You may wish to attach the main.log files for boost and gtk2 as referenced in the above error messages; perhaps they contain useful information.

[raramayo (Rodolfo Aramayo)]

In another machine I obtained

--->  Building inkscape
Error: Target org.macports.build returned: shell command failed
Log for inkscape is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_graphics_inkscape/main.log
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>

genomics08:~ raramayo$ sudo port install Inkscape
Password:
sudo: Can't mkdir /var/db/sudo/raramayo: File exists
sqlite error: SQL logic error or missing database (1) while executing query: CREATE TEMPORARY TABLE items (refcount, proc UNIQUE, name, url, path, worker, options, variants)
    while executing
"registry::open $db_path"
    (procedure "mportinit" line 536)
    invoked from within
"mportinit ui_options global_options global_variations"
Error: /opt/local/bin//port: Failed to initialize MacPorts, sqlite error: SQL logic error or missing database (1) while executing query: CREATE TEMPORARY TABLE items (refcount, proc UNIQUE, name, url, path, worker, options, variants)

Unfortunately the log file is empty

[ryandesign (Ryan Carsten Schmidt)]

The relevant error from the main.log might be:

:info:build ldld:: in in libinkscape.a , libinkscape.afile,  too filesmall
:info:build too small

That's the parallel build encountering the same error twice and intermingling the responses. If we clean that up, it should read:

:info:build ld: in libinkscape.a, file too small
:info:build ld: in libinkscape.a, file too small

What version of Xcode is installed? If you have a very old version of Xcode (i.e. earlier than the earliest supported by Snow Leopard, which is 3.2), that might account for the very strange behavior you're seeing. ​The current version is 3.2.4. If you have less, you should upgrade.

Is your hard disk ok? Run Disk Utility and verify the disk.

It might be helpful if we would stop mixing problems from several different machines in one bug report, since you seem to be having different problems on each machine and we'll likely have to tackle each of them separately.

[raramayo (Rodolfo Aramayo)]

Replying to ryandesign@…:

The relevant error from the main.log might be:

:info:build ldld:: in in libinkscape.a , libinkscape.afile,  too filesmall
:info:build too small

That's the parallel build encountering the same error twice and intermingling the responses. If we clean that up, it should read:

:info:build ld: in libinkscape.a, file too small
:info:build ld: in libinkscape.a, file too small

What version of Xcode is installed? If you have a very old version of Xcode (i.e. earlier than the earliest supported by Snow Leopard, which is 3.2), that might account for the very strange behavior you're seeing. ​The current version is 3.2.4. If you have less, you should upgrade.

I have version 3.2.3. And I am using a "fresh" installation of 10.6.4. Now, very importantly, I installed the system using NetBoot. This is, I configured a computer, made a carboncopy cloner copy and then used my server to create a netrestore image of the hard disk. This is the only thing different from other MacPorts installation I made before.

Is your hard disk ok? Run Disk Utility and verify the disk.

OH Yes, my disks are OK and I run DK on them routinely

It might be helpful if we would stop mixing problems from several different machines in one bug report, since you seem to be having different problems on each machine and we'll likely have to tackle each of them separately.

I agree and I apologize. I have never seen MacPorts act like this before....

[jmroot (Joshua Root)]

I really can't see how our code could be causing filesystem problems like these. I'd be looking for some misconfiguration, corruption or hardware fault on the affected machine.

BTW, it looks like you're running an outdated trunk build in comment:3.

[ryandesign (Ryan Carsten Schmidt)]

I am aware of what NetBoot is, but have never used it, and have not heard of anyone else using it with MacPorts. Perhaps that doesn't work. Can you try without NetBoot -- just booting from, and having MacPorts installed on, the internal hard drive?

[raramayo (Rodolfo Aramayo)]

Replying to ryandesign@…:

I am aware of what NetBoot is, but have never used it, and have not heard of anyone else using it with MacPorts. Perhaps that doesn't work. Can you try without NetBoot -- just booting from, and having MacPorts installed on, the internal hard drive?

People,

I was looking into this. I believe that this strange behavior is related not to NetBoot, but to the fact that the computers that are running into trouble they all have "Mobile Accounts" and therefore are linked to an "Network Account Server" In other words they all listen to an LDAPv3 server.
Something FUNDAMENTALLY different happenes when computers are "Mobile Accounts Active" For example, on a regular system, on the terminal you can do a "sudo su" and get the "sh-3.2#" prompt. However on these computers if you type "sudo su" you are prompted for your passwd and then the system says: "su: sorry"

Now if I issue a command like: "sudo something" the system asks for passwd and then acts normally.

In most of the "complains" I got from MacPorts ports during installation they all mentioned having problems with "sudoers file"

In addition, when the commands were repeated, most times they went fine the second time.

I am going to ask a student of mine to reformat and re-install the OS in one machine and then test MacPorts without activating "Mobile Accounts"

Very Mac users use the power of mobile accounts and that is why, I suspect, these behaviors went undetected

I should say that I made the same installation on my laptop and on my server and in both cases MacPorts behave as expected

I have upgraded XCode to the latest version, but I doubt this was the culprit

Thanks for your help/advice

[jmroot (Joshua Root)]

We can't do anything about sudo not working.