Safari windows invisible

Did you reinstall Safari as that thread advised?

Before going any further I would back up all data to another computer or exteranal drive.

Have you tried deleting all Safari preference files?

Susan Hull wrote:

-Ran BitDefender for 12 hours before giving up--all its hits were files from an Entourage archive that is stored on my backup drive by Time Machine, and all said they could not be quarantined or deleted.

Generally speaking, there is no need to scan your backup drives. If and when you find malware on your main drive, you should simultaneously delete those files from backup using the backup utility and not the Finder. Doing the latter will almost certainly render your backup unusable. I assume you know that the Entourage archive is one huge file that contains all your e-mail, etc. and if BitDefender had been able to do anything with it you would have lost everything.

-Ran ClamXav, which reviews said was more compatible with Snow Leopard. Many hits, all but a handful being Outlook messages. Two notes: I was only offered my own user to scan in ClamXav; couldn't scan the whole HD. And, the hits from the two anti-malware apps were altogether different. Makes one wonder...

I don't use Outlook 2011 yet, so I'm not sure whether it stores e-mail as individual messages now or still uses the old model of one huge databse. Either way, you need to be cautious with any e-mail infections ClamXav finds. You should never allow ClamXav (or any other A-V software) to move or delete e-mails as this will corrupt the mailbox index (and as I said could cause you to lose everything with certain e-mail clients). It may also leave the original message on the e-mail server, depending on the type account you have and certain preferences on the server and your client.

The correct way is to right-click/control-click on the infection or file name and select "Reveal In Finder". If it's an individual message, then double-click it to open in Outlook, read the message to make certain it was correctly identified as junk/spam/phishing (especially if Heuristics was used to identify it) and either use the Outlook delete function to delete it from both your hard drive and server or if you need to keep the message, return to ClamXav and tell it to ignore the file in future scans.

If you already allowed ClamXav to quarantine/delete those files, then you will need to rebuild the mailboxes that they came from. Your Scan Log can tell you where they were if you don't know. They may also show up again when you next check for mail if they were left on the server.

I don't know anything about BitDefender for Mac. They had a good reputation with Windows but along with several other A-V vendors are new to Mac OS X, so I hesitate to recommend any of those until they have proven they understand the Mac environment. I can only guess why the results might be different.

Susan Hull wrote:

I was only offered my own user to scan in ClamXav; couldn't scan the whole HD.

Sorry, forgot to address this.

Yes, ClamXav has always been designed as a per user scanner for security purposes and will only scan files you have read access to. If you're an admin then you will be able to scan anything an admin can but won't be able to scan directories you don't have read access to, such as other user's documents and a few corners of the operating system.

HI Susan ..

So, Safari will open and the menu bar appear, but no Safari windows, prefs window, or About window (no title bars, nothing). Opening a new window via Command-N or from menu produces nothing on screen, but the window will appear in the list of open windows in the dropdown Window menu. Ditto for a bookmarked or History item--all show up in Windows menu dropdown as they would normally, but all are simply missing on screen. Help, Downloads, and Activity windows open and are visible.The only extensions I have installed are AdBlock and a Flash blocker (though window listing extensions is invisible, too, so can't double check). Definitely no toolbar except the usual Google (which I think comes with, not an add-on, right?).

Try troubleshooting Safari: Unsupported third-party add-ons may cause Safari to unexpectedly quit or have performance issues

Since then:

-Sev HD reboots, sev Safari relaunches, both from dock and from Apps window

-Ran Disk First Aid from CD, repaired a zillion permissions, but no HD problems found.

If third party plugins aren't the issue, just so you are aware, just verying permissions does not veriy the startup disk for errors.

Launch Disk Utility. Select the startup disk on the left.

Click Verify Disk (not Verify Disk Permissions)

If necessary, click Repair Disk.

If the startup disk appears to be ok, try Starting up in Safe Mode

A Safe Mode boot takes longer than a normal boot so be patient. Once you see the Desktop click the Apple menu icon top left corner in your screen. From the drop down menu click Restart.

Then try Safari.

OS X viruses are relatively rare and I suspect your problems are unrelated to viruses.

It is not uncommon to instruct virus checkers to ignore email. If I remember correctly ClamXav is incompatible with some email clients.

After backing up I would run AppleJack with the following instruction:

applejack AUTO shutdown

Neville Hillyer wrote:

If I remember correctly ClamXav is incompatible with some email clients.

Not incompatible, but can be a PITA with certain email clients that use a single database. That generally holds true for all A-V software.

I used to use ClamXav with Thunderbird pop. It clashed with Thunderbird until I stoped it checking email as ClamXav advised. Thunderbird does not use a database - it uses traditional mbox files - these are long text files containing many emails one after the other with simple text delimiters.

I used have used several other virus checkers and none had difficulties with email.

For the record: Manually removing a complete email from mbox files does not cause corruption.

Sorry Susan - I should have said quit from Safari before removing preference files. It would be best to do it again just in case the open Safari returned some old data to the file at the point of quitting.

Regrettably Safari versions 5.1 and later appear to be having more difficulties that one would expect - hopefully these will be resolved.

Neville Hillyer wrote:

I used to use ClamXav with Thunderbird pop. It clashed with Thunderbird until I stoped it checking email as ClamXav advised. Thunderbird does not use a database - it uses traditional mbox files - these are long text files containing many emails one after the other with simple text delimiters.

Thanks for that. I knew that it somehow aggregated messages, but wasn't certain how. Still makes finding the exact message being reported as infected more difficult. OTOH, it makes the file small enough that it can be scanned by the clamav engine which has file size limits. You say traditional. Are you aware of any other clients that use that technique?

For the record: Manually removing a complete email from mbox files does not cause corruption.

I would assume because there is no index involved. But at the same time if you allowed ClamXav to move or delete it, the entire mobox would get moved/deleted, thus requiring manual or client processing.

I think that originally all email clients used mbox. Sun used it on its Unix servers and it was practical to manually move a whole mbox file with 10,000 messages or more from server to client without downloading the messages one at a time.

Clients such as Eudora used a modified mbox - it extracted attachments and put them in a separate directory.

Thunderbird uses index files with an msf extension - if an incompatibility is detected it rebuilds the index from the mbox file.

I should have said that it is relatively rare for viruses to harm OS X.

It is not so rare for Windows viruses to be transferred to OS X by various means.