Database stuff appearing in the trash. Anyone know what it is?

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Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
Database.sqlite3, Database.sqlite3-journal have started appearing in the trash on my drive. I have never seen them before and they show up every few minutes. I have been looking for the source and cannot find it. I know that the app that creates them is a data base used by a lot of companies, including Apple. However I have never seen them appear like this.

I have been able to open the Journal file in TextEdit and it shows nonsense characters. The files are really small. Is there any way to discover the source of these reports?

Bear😎



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Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
I’m not trying to be a pill but now there are 5 of these databases in my trash and I deleted all of them only 10 minutes ago.

Bear😎

---------- Forwarded message ----------
From: John Turner <[hidden email]>
Date: Jul 13, 2017, 5:14 PM -0400
To: TidBITS Talk <[hidden email]>
Subject: Database stuff appearing in the trash. Anyone know what it is?

Database.sqlite3, Database.sqlite3-journal have started appearing in the trash on my drive. I have never seen them before and they show up every few minutes. I have been looking for the source and cannot find it. I know that the app that creates them is a data base used by a lot of companies, including Apple. However I have never seen them appear like this.

I have been able to open the Journal file in TextEdit and it shows nonsense characters. The files are really small. Is there any way to discover the source of these reports?

Bear😎



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Re: Database stuff appearing in the trash. Anyone know what it is?

David Ross
In reply to this post by "John Turner the Bear😎"
On 7/13/17 5:14 PM, John Turner wrote:
Database.sqlite3, Database.sqlite3-journal have started appearing in the trash on my drive. I have never seen them before and they show up every few minutes. I have been looking for the source and cannot find it. I know that the app that creates them is a data base used by a lot of companies, including Apple. However I have never seen them appear like this.

I have been able to open the Journal file in TextEdit and it shows nonsense characters. The files are really small. Is there any way to discover the source of these reports?
Start by letting us know what OS version you're running.

David



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Re: Database stuff appearing in the trash. Anyone know what it is?

Chris Devers
In reply to this post by "John Turner the Bear😎"
SQLite ( https://en.wikipedia.org/wiki/SQLitehttps://www.sqlite.org/) is a public domain database engine. 

Note that it's not just "open source" — the guy that wrote it specifically donated it as public property. You own it as much as he does.

By comparison, normal free/open source software license place certain restrictions on how the software & source code can be used, but there’s no restrictions of any kind on SQLite, because it belongs to everybody, in much the same way National Parks or the oceans do. This is a pretty radical thing to do, and I can think of few if any other free software projects that have done this.

Because of the completely free & open nature of SQLite, lots of software uses it — why bother implementing your own storage software, when you can just embed SQLite and let it handle it for you? 

Therefore, it’s close to impossible to say, based on what you’ve told us, what software on your computer is making these databases. 

You aren't going to figure out what’s in these databases by using TextEdit, because that's a text editor, and these aren't text documents but database binary files.. But there are lots of free GUIs for handling SQLite files — you can start with the two URLs above, for starters — so it shouldn't be hard to get a sense of what kind of information is in them, if you're really curious. 

-- 
Chris Devers



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Re: Database stuff appearing in the trash. Anyone know what it is?

Al Varnell
On Thu, Jul 13, 2017 at 06:32 PM, Chris Devers wrote:
there are lots of free GUIs for handling SQLite files

Two free ones that I use frequently:
DB Browser for SQLite <http://sqlitebrowser.org>.

-Al-
-- 
Al Varnell
Mountain View, CA







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Re: Database stuff appearing in the trash. Anyone know what it is?

Brian L. Matthews
In reply to this post by "John Turner the Bear😎"
On 7/13/17 5:19 PM, John Turner wrote:
I have no clue! I have been unable to find where they are being generated from. All I know is that they are being generated. I checked online the app that creates them is called Database.sqlite. According to the site it is free, open source, lots of companies use it…including Apple. Beyond that I cannot get any answers. Whatever the source they have appeared at about 10 an hour, so something is monitoring something…but what it is I have no idea.

Database.sqlite3, Database.sqlite3-journal have started appearing in the trash on my drive. I have never seen them before and they show up every few minutes. I have been looking for the source and cannot find it. I know that the app that creates them is a data base used by a lot of companies, including Apple. However I have never seen them appear like this.

I have been able to open the Journal file in TextEdit and it shows nonsense characters. The files are really small. Is there any way to discover the source of these reports?

Bear😎

Which app is creating them?

Brian

Ah, I misunderstood "I know that the app that creates them is a..."

SQLite is a database engine (or library). It is used by lots of applications, including Apple's, but isn't a standalone application on its own.

Anyways, if I google "mac os x something leaving Database.sqlite3 files in the trash", the second link result is from <https://discussions.apple.com/thread/1201041?tstart=0>, which is a discussion on Apple's discussion forums of what sounds like the same problem. Read through that and see if anything there helps.

Brian



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Re: Database stuff appearing in the trash. Anyone know what it is?

Al Varnell
On Thu, Jul 13, 2017 at 07:11 PM, Brian L. Matthews wrote:
I google "mac os x something leaving Database.sqlite3 files in the trash", the second link result is from <https://discussions.apple.com/thread/1201041?tstart=0>, which is a discussion on Apple's discussion forums of what sounds like the same problem. Read through that and see if anything there helps.

Hopefully the OP will get more out of that ten year old, locked, un-solved close to fifty entry discussion than I did.

There are clues that it might be due to dot mac syncing, something that hasn't been available for many years now. Also might have something to do with Safari or Mail and RSS, but as far as I could see, nothing definitive.

-Al-
-- 
Al Varnell
Mountain View, CA







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Re: Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
I have deleted every database journal or file that I could find except what Apple requires for Sierra 12.5.

I reinstalled a new OS. I have blocked Crash Report from being shared with Apple or anyone else. I have blocked any update downloads from anyone but Apple. I have no RSS capability installed. There is no Google, Microsoft etc. Deleted every cache, app, font etc.

Downloaded the apps suggested to look at the files and they will not tell me the source of the databases.

Checked the Apple Community discussions as suggested and there were no answers. The problem has occurred since 10.5 for a lot of Mac users. An new report of the problems was reported on the Sierra page a few weeks ago for Sierra 12.5…no resolution has been provided.

The Bear😎

On Jul 13, 2017, 11:00 PM -0400, Al Varnell <[hidden email]>, wrote:
On Thu, Jul 13, 2017 at 07:11 PM, Brian L. Matthews wrote:
I google "mac os x something leaving Database.sqlite3 files in the trash", the second link result is from <https://discussions.apple.com/thread/1201041?tstart=0>, which is a discussion on Apple's discussion forums of what sounds like the same problem. Read through that and see if anything there helps.

Hopefully the OP will get more out of that ten year old, locked, un-solved close to fifty entry discussion than I did.

There are clues that it might be due to dot mac syncing, something that hasn't been available for many years now. Also might have something to do with Safari or Mail and RSS, but as far as I could see, nothing definitive.

-Al-
-- 
Al Varnell
Mountain View, CA






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Re: Database stuff appearing in the trash. Anyone know what it is?

@lbutlr
In reply to this post by "John Turner the Bear😎"
On 13 Jul 2017, at 16:45, John Turner <[hidden email]> wrote:
> I’m not trying to be a pill but now there are 5 of these databases in my trash and I deleted all of them only 10 minutes ago.

I nearly never look in my trash, but I've never seen this behavior (and I don't have any in my trash now, last emptied about a week ago).

If you select the file in the trash and use the file menu "Put Back" command it may put it back where it came from, letting you know, possibly, what is creating them. If not, get info will at least tell you what disk they came from.

SQLite is included with OS X (er.. macOS I'm never going to get used to that) and is used for a variety of things, most famously the index files for Mail.app, but many other things as well.

You can also, in the Terminal, try

 mdfind -name Database.sqlite3

And that will tell you all the places that filename exists, which might also be a clue.

(the only file with that name I have in my system is in ~/Library/PubSub/Database/Database.sqlite3, which is part of the background syncing iCloud does for Safari.)

However, why is this a problem in the first place? The files will be deleted when you empty your trash.

--
Apple broke AppleScripting signatures in Mail.app, so no random signatures.




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Re: Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
Oh yes, you can empty the trash and they are gone, and in a few minutes new data bases are created. Mail is not active and terminal furnished no details regarding the source. And, I do not synch anything to the iCloud either. Still no help from Apple and no answers from the Apple Community. I do have two apps that definitely use the DataBase but when you delete the files they use the apps are disabled…Spark (my eMail app and MiniNote Pro 5.0). I’ve tried to track the files to them but it does not seem likely that they are responsible since I have been using these apps for a year and the problem just appeared a couple about 4 days ago.

The Bear😎

On Jul 14, 2017, 6:50 PM -0400, @lbutlr <[hidden email]>, wrote:
On 13 Jul 2017, at 16:45, John Turner <[hidden email]> wrote:
I’m not trying to be a pill but now there are 5 of these databases in my trash and I deleted all of them only 10 minutes ago.

I nearly never look in my trash, but I've never seen this behavior (and I don't have any in my trash now, last emptied about a week ago).

If you select the file in the trash and use the file menu "Put Back" command it may put it back where it came from, letting you know, possibly, what is creating them. If not, get info will at least tell you what disk they came from.

SQLite is included with OS X (er.. macOS I'm never going to get used to that) and is used for a variety of things, most famously the index files for Mail.app, but many other things as well.

You can also, in the Terminal, try

mdfind -name Database.sqlite3

And that will tell you all the places that filename exists, which might also be a clue.

(the only file with that name I have in my system is in ~/Library/PubSub/Database/Database.sqlite3, which is part of the background syncing iCloud does for Safari.)

However, why is this a problem in the first place? The files will be deleted when you empty your trash.

--
Apple broke AppleScripting signatures in Mail.app, so no random signatures.




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Re: Database stuff appearing in the trash. Anyone know what it is?

Mr. Seth Anderson

On Jul 14, 2017, at 5:59 PM, [hidden email] wrote:

Oh yes, you can empty the trash and they are gone, and in a few minutes new data bases are created. Mail is not active and terminal furnished no details regarding the source. And, I do not synch anything to the iCloud either

I don’t have a solution, just a “me too” (albeit a while ago so I don’t remember what I did to solve this). Have you tried logging in as a different user? Booting into “Safe Mode”?

It would seem that since something is creating these files, and deleting them, the first step would be in ascertaining what app creates them by process of elimination. 


-Seth Anderson
sursum vestri culus

often found at 

or





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Re: Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
Thanks Seth,

I have been trying to locate the app that is doing this, and so far have been unable to. Safe Mode has not helped to solve the problem either. This problem started about 4 days ago. I have deleted all of the apps, caches, containers etc. for that period to no avail.

The Bear😎

On Jul 14, 2017, 9:17 PM -0400, Mr. Seth Anderson <[hidden email]>, wrote:

On Jul 14, 2017, at 5:59 PM, [hidden email] wrote:

Oh yes, you can empty the trash and they are gone, and in a few minutes new data bases are created. Mail is not active and terminal furnished no details regarding the source. And, I do not synch anything to the iCloud either

I don’t have a solution, just a “me too” (albeit a while ago so I don’t remember what I did to solve this). Have you tried logging in as a different user? Booting into “Safe Mode”?

It would seem that since something is creating these files, and deleting them, the first step would be in ascertaining what app creates them by process of elimination. 


-Seth Anderson
sursum vestri culus

often found at 

or




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Re: Database stuff appearing in the trash. Anyone know what it is?

Alan Forkosh
Have you checked the various logs via the Console app? That might provide a clue as to what was active when the db’s were trashed.

Alan Forkosh                    Oakland, CA
[hidden email]
http://al4kosh.com



On Jul 14, 2017, at 6:24 PM, [hidden email] wrote:

Thanks Seth,

I have been trying to locate the app that is doing this, and so far have been unable to. Safe Mode has not helped to solve the problem either. This problem started about 4 days ago. I have deleted all of the apps, caches, containers etc. for that period to no avail.

The Bear😎

On Jul 14, 2017, 9:17 PM -0400, Mr. Seth Anderson <[hidden email]>, wrote:

On Jul 14, 2017, at 5:59 PM, [hidden email] wrote:

Oh yes, you can empty the trash and they are gone, and in a few minutes new data bases are created. Mail is not active and terminal furnished no details regarding the source. And, I do not synch anything to the iCloud either

I don’t have a solution, just a “me too” (albeit a while ago so I don’t remember what I did to solve this). Have you tried logging in as a different user? Booting into “Safe Mode”?

It would seem that since something is creating these files, and deleting them, the first step would be in ascertaining what app creates them by process of elimination. 


-Seth Anderson
sursum vestri culus

often found at 

or




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Re: Database stuff appearing in the trash. Anyone know what it is?

Brian L. Matthews
In reply to this post by "John Turner the Bear😎"
On 7/14/17 6:24 PM, [hidden email] wrote:
 > Thanks Seth,
 >
 > I have been trying to locate the app that is doing this, and so far
have been unable to. Safe Mode has not helped to solve the problem
either. This problem started about 4 days ago. I have deleted all of the
apps, caches, containers etc. for that period to no avail.

Have you tried lsof? Something like:

$ lsof +c0 | grep Database.sqlite3

(run /Applications/Utilities/Terminal then paste everything except the
initial "$ " into the Terminal window and hit return) will tell you
which applications have a file called Database.sqlite3 open when you run
the commands.

Brian


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Re: Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
Thanks Brian!

What I found is a Directory that contains the newly generated database, still not the source. Without a doubt there is only one app or what have you that is doing it. I still have not located it. Do you have another command in mind?

Bear😎

On Jul 15, 2017, 2:55 AM -0400, Brian L. Matthews <[hidden email]>, wrote:
On 7/14/17 6:24 PM, [hidden email] wrote:
Thanks Seth,

I have been trying to locate the app that is doing this, and so far
have been unable to. Safe Mode has not helped to solve the problem
either. This problem started about 4 days ago. I have deleted all of the
apps, caches, containers etc. for that period to no avail.

Have you tried lsof? Something like:

$ lsof +c0 | grep Database.sqlite3

(run /Applications/Utilities/Terminal then paste everything except the
initial "$ " into the Terminal window and hit return) will tell you
which applications have a file called Database.sqlite3 open when you run
the commands.

Brian



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Re: Database stuff appearing in the trash. Anyone know what it is?

Curtis Wilcox
On Jul 15, 2017, at 6:52 AM, [hidden email] wrote:

Thanks Brian!

What I found is a Directory that contains the newly generated database, still not the source. Without a doubt there is only one app or what have you that is doing it. I still have not located it. Do you have another command in mind?

I don't know what the "+c0" parameter does but normally the lsof command outputs starts with a process name, try piping the output of 'lsof' without parameters to grep the filename:

sudo lsof | grep Database.sqlite3

I haven't been closely following this thread but on my Mac running Sierra, I only found a file named Database.sqlite3 at ~/Library/PubSub/Database/Database.sqlite3. Mine hasn't been changed since 2013 (I've migrated this user profile a number of times).

If the directory you found Database.sqlite3 is not the same as mine, where is yours?

PubSub is a "Utility for managing RSS/Atom subscriptions via the PubSub framework." It is, or has been, used by a number of Apple applications that do, or did, use RSS feeds.

pubsub is a command line program for PubSub that might be useful. 'pubsub list clients' will list the signatures of applications that can or have used it; on mine it lists: 

#Feeds Signature
 0 com.apple.Safari
 0 com.apple.mail
 0 com.apple.screensaver.rssdotmacpictures
 0 com.apple.Xcode

If you have one or more with subscriptions, which ones? Some of the applications in my list either don't exist or may not support RSS feed reading anymore; Safari does feed reading but I think Mail dropped it quite a while ago. 




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Re: Database stuff appearing in the trash. Anyone know what it is?

David Ross
In reply to this post by "John Turner the Bear😎"
This may be a normal behavior that Apple or some vendor doesn't feel
needs documenting.

I.E. not a problem.

On 7/14/17 9:24 PM, [hidden email] wrote:
> This problem started about 4 days ago.



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Re: Database stuff appearing in the trash. Anyone know what it is?

Alexander Forbes

On Jul 15, 2017, at 7:18 AM, David Ross <[hidden email]> wrote:

This may be a normal behavior that Apple or some vendor doesn't feel needs documenting.

I.E. not a problem.

I agree. The question was asked yesterday, where is the problem with sqlLite files found in the trash? How is a problem evidenced elsewhere? Why reinstall the OS in unsuccessful attempt to make it go away?




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Re: Database stuff appearing in the trash. Anyone know what it is?

Curtis Wilcox
In reply to this post by Curtis Wilcox
[John replied to me off-list but ok'd me replying on]

On Jul 15, 2017, at 10:08 AM, [hidden email] wrote:

Hi Curtis!

Thanks so much for your help so early on a Saturday morning. I ran Terminal with your command. I am not a programmer and I do not understand the results, I’m enclosing a copy. If you get a chance and feel like it would you tell me what is means?

Last login: Sat Jul 15 09:37:25 on console
Johns-Mac-mini:~ johnturner$ sudo lsof | grep Database.sqlite3
Password:
Johns-Mac-mini:~ johnturner$ sudo lsof | grep Database.sqlite3
Johns-Mac-mini:~ johnturner$ pubsub list clients
07/15/17 10:05:55.164: 669 [WARNING] IPC call returned (ipc/mig) server died (11,4294966988) (Mach error fffffecc)
07/15/17 10:05:55.164: 669 [WARNING] Foundation::NetException "(ipc/mig) server died (11,4294966988)" caught in static void PubSub::ClientCore::openClientSession()
07/15/17 10:05:55.165: 669 [WARNING] std::exception "std::exception" caught in +[PSClient allClientBundleIdentifiers]
#Feeds Signature
07/15/17 10:05:55.166: 669 [WARNING] IPCClient: Server port 10759 is invalid; looking it up again...
07/15/17 10:06:05.228: 669 [WARNING] IPC call returned (ipc/mig) server died (11,4294966988) (Mach error fffffecc)
07/15/17 10:06:05.228: 669 [WARNING] Foundation::NetException "(ipc/mig) server died (11,4294966988)" caught in static void PubSub::ClientCore::openClientSession()
07/15/17 10:06:05.229: 669 [WARNING] std::exception "std::exception" caught in +[PSClient allClientBundleIdentifiers]
Johns-Mac-mini:~ johnturner$ 

Thanks again!

It looks like you ran the first command twice and neither time had any output. That's not really surprising, if the file isn't open at the moment lsof is run, there's nothing to show. But running Brian's command did output a directory path, suggesting the file was open at that time?

I can't explain the details of the output from running 'pubsub list clients', but it indicates there's a problem with PubSub and suggests that PubSub is what's putting the Database.sqlite3 file in the Trash.

Do you know if Safari or any other application is subscribed to RSS feeds?




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Re: Database stuff appearing in the trash. Anyone know what it is?

"John Turner the Bear😎"
I have no RSS apps or functions on my Mac at all. Guys I thank you all for your help! I am just going to let things be. We all have wasted too much time on this. It is what it is and I am just to damn old to waste any more energy on it. My wife’s gut level suspicion is that it is Apple that is creating the DB. Who knows? But I promise not to mention this problem ever again! Promise!

Bear😎

On Jul 15, 2017, 12:43 PM -0400, Curtis Wilcox <[hidden email]>, wrote:
[John replied to me off-list but ok'd me replying on]

On Jul 15, 2017, at 10:08 AM, [hidden email] wrote:

Hi Curtis!

Thanks so much for your help so early on a Saturday morning. I ran Terminal with your command. I am not a programmer and I do not understand the results, I’m enclosing a copy. If you get a chance and feel like it would you tell me what is means?

Last login: Sat Jul 15 09:37:25 on console
Johns-Mac-mini:~ johnturner$ sudo lsof | grep Database.sqlite3
Password:
Johns-Mac-mini:~ johnturner$ sudo lsof | grep Database.sqlite3
Johns-Mac-mini:~ johnturner$ pubsub list clients
07/15/17 10:05:55.164: 669 [WARNING] IPC call returned (ipc/mig) server died (11,4294966988) (Mach error fffffecc)
07/15/17 10:05:55.164: 669 [WARNING] Foundation::NetException "(ipc/mig) server died (11,4294966988)" caught in static void PubSub::ClientCore::openClientSession()
07/15/17 10:05:55.165: 669 [WARNING] std::exception "std::exception" caught in +[PSClient allClientBundleIdentifiers]
#Feeds Signature
07/15/17 10:05:55.166: 669 [WARNING] IPCClient: Server port 10759 is invalid; looking it up again...
07/15/17 10:06:05.228: 669 [WARNING] IPC call returned (ipc/mig) server died (11,4294966988) (Mach error fffffecc)
07/15/17 10:06:05.228: 669 [WARNING] Foundation::NetException "(ipc/mig) server died (11,4294966988)" caught in static void PubSub::ClientCore::openClientSession()
07/15/17 10:06:05.229: 669 [WARNING] std::exception "std::exception" caught in +[PSClient allClientBundleIdentifiers]
Johns-Mac-mini:~ johnturner$ 

Thanks again!

It looks like you ran the first command twice and neither time had any output. That's not really surprising, if the file isn't open at the moment lsof is run, there's nothing to show. But running Brian's command did output a directory path, suggesting the file was open at that time?

I can't explain the details of the output from running 'pubsub list clients', but it indicates there's a problem with PubSub and suggests that PubSub is what's putting the Database.sqlite3 file in the Trash.

Do you know if Safari or any other application is subscribed to RSS feeds?



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