Got my ports tree deleted after attempting ports update

[bsdnotbdsm]

Hello,
The following happened on my FreeBSD 9.1 virtual machine which had the full ports tree in place under /usr/ports:

[root@virtbsd91 ~]# portsnap fetch && portsnap update && portmaster -ad                                                                                                                                                          
Looking up portsnap.FreeBSD.org mirrors... 7 mirrors found.                                                                                                                                                                      
Fetching snapshot tag from ec2-eu-west-1.portsnap.freebsd.org... done.                                                                                                                                                           
Fetching snapshot metadata... done.                                                                                                                                                                                              
Updating from Mon May 12 14:22:54 CEST 2014 to Fri May 16 01:08:12 CEST 2014.                                                                                                                                                    
Fetching 4 metadata patches... done.                                                                                                                                                                                             
Applying metadata patches... done.                                                                                                                                                                                               
Fetching 0 metadata files... done.                                                                                                                                                                                               
Fetching 402 patches.....10....20....30....40....50....60....70....80....90....100....110....120....130....140....150....160....170....180....190....200....210....220....230....240....250....260....270....280....290....300....310....320....330....340....350....360....370....380....390....400. done.                                                                                                                                                       
Applying patches... done.                                                                                                                                                                                                        
Fetching 18 new ports or files... done.                                                                                                                                                                                          
Removing old files and directories... done.                                                                                                                                                                                      
Extracting new files:                                                                                                                                                                                                            
comm: /usr/ports/.portsnap.INDEX: No such file or directory                                                                                                                                                                      
/usr/sbin/portsnap: cannot create /usr/ports/.portsnap.INDEX: No such file or directory                                                                                                                                          
Building new INDEX files... /usr/sbin/portsnap: cannot create /usr/ports/INDEX-7: No such file or directory                                                                                                                      
[root@virtbsd91 ~]# 
[root@virtbsd91 ~]# 
[root@virtbsd91 ~]# portsnap fetch && portsnap update && portmaster -ad
Looking up portsnap.FreeBSD.org mirrors... 7 mirrors found.
Fetching snapshot tag from ec2-eu-west-1.portsnap.freebsd.org... done.
Ports tree hasn't changed since last snapshot.
No updates needed.
/usr/ports was not created by portsnap.
You must run 'portsnap extract' before running 'portsnap update'.
[root@virtbsd91 ~]# ls /usr/    
bin/     games/   home/    include/ lib/     lib32/   libdata/ libexec/ local/   obj/     sbin/    share/   src/     
[root@virtbsd91 ~]# ls /usr/ports/
ls: /usr/ports/: No such file or directory

These are machine details:
[root@virtbsd91 ~]# uname -a

FreeBSD virtbsd91 9.1-RELEASE-p11 FreeBSD 9.1-RELEASE-p11 #0: Tue Apr  8 20:54:56 UTC 2014     root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC  amd64

Of course I did NOT delete ports tree myself:

[root@virtbsd91 ~]# history |grep rm |grep port |grep -v grep
[root@virtbsd91 ~]#

So, what happened with the ports tree?! How is it posible to be deleted during normal upgrade operation?! Needless to say, I never experienced such situation before.
Anyone experienced similar situation?

If yes, please reply. I'm trying to understand what went wrong there.

Regards.

[J65nko]

I think the solution can be found in these error messages that you got:

No updates needed.
/usr/ports was not created by portsnap.
You must run 'portsnap extract' before running 'portsnap update'.

An possible error could be caused by insufficient disk space. What is the ouput of # df -h?

[bsdnotbdsm]

Hello,
Thanks for the reply first of all.
All ended up well in the end.
Indeed "mkdir /usr/ports && cd /usr/ports && portsnap extract" fixed the issue.

Disk space is not a problem, this is the status after(!) extracting ports tree:

[root@virtbsd91 ~]# df -m
Filesystem    1M-blocks Used Avail Capacity  Mounted on
/dev/ada0p2        9905 5740  3372    63%    /
devfs                 0    0     0   100%    /dev

I think the main problem (root cause) was a / filesystem corruption I had 1 week ago, that prevented me to boot. I fixed it with fsck /dev/ada0p2 but without using journal. After fsck fix, system booted up, but it seems some index files required by portsnap were deleted.
With regards to the error messages that I've posted in the first post of this thread, this is the relevant section which seems to be the stopper for extracting the ports tree:

Extracting new files:
comm: /usr/ports/.portsnap.INDEX: No such file or directory
/usr/sbin/portsnap: cannot create /usr/ports/.portsnap.INDEX: No such file or directory

Anyway, after re-extracting the ports tree, all is OK like before. The database with installed packages was not affected, so I could just continue the ports update operation, like nothing happened.

And yes, again with regards to the errors, and as a final proof that a missing file was the issue, this is the current status:

[root@virtbsd91 ~]# ls -al /usr/ports/.portsnap.INDEX
-rw-r--r--  1 root  wheel  2107349 May 18 13:29 /usr/ports/.portsnap.INDEX

So: Problem solved!