From sokol at insa-toulouse.fr  Thu Jul  6 11:21:54 2017
From: sokol at insa-toulouse.fr (Serguei Sokol)
Date: Thu, 6 Jul 2017 11:21:54 +0200
Subject: [Rd] [New Patch] Fix disk corruption when writing
In-Reply-To: <fe2b1e03-2f57-820e-6226-217be4184907@insa-toulouse.fr>
References: <CAPXDfF=770SgtaLoMeaF7XGUfj3wFSU6hUn6ZFrds0VnwG_+zA@mail.gmail.com>
 <ba1bb252-8524-ce6d-b0d7-0d66a09789d2@gmail.com>
 <CA+A1kV5xB3yfD2SnKenrnrfgV6wDObQW8vFMxUVQd2kxTc0BjQ@mail.gmail.com>
 <1093380f-a632-ce28-af21-a87e1a40a8db@gmail.com>
 <8ede4416-7745-e66c-7d2f-53c04f1a9067@insa-toulouse.fr>
 <fe2b1e03-2f57-820e-6226-217be4184907@insa-toulouse.fr>
Message-ID: <0783f593-8624-6f3f-7c54-eb3ab2938a48@insa-toulouse.fr>

I propose the following patch against the current R-devel/src/main/connection.c (cf. attached file).
It gives (on my linux box):
 > fc=file("/dev/full", "w")
 > write.csv("a", file=fc)
Error in writeLines(paste(col.names, collapse = sep), file, sep = eol) :
   system call failure on writing
 > close(fc)

Serguei.

Le 05/07/2017 ? 15:33, Serguei Sokol a ?crit :
> Le 05/07/2017 ? 14:46, Serguei Sokol a ?crit :
>> Le 05/07/2017 ? 13:09, Duncan Murdoch a ?crit :
>>> On 05/07/2017 5:26 AM, January W. wrote:
>>>> I tried the newest patch, but it does not seem to work for me (on
>>>> Linux). Despite the check in Rconn_printf, the write.csv happily writes
>>>> to /dev/full and does not report an error. When I added a printf("%d\n",
>>>> res); to the Rconn_printf() definition, I see only positive values
>>>> returned by the vfprintf call.
>>>>
>>>
>>> That's likely because you aren't writing enough to actually trigger a write to disk during the write.  Writes are buffered, and the error doesn't happen 
>>> until the buffer is written.
>> I can confirm this behavior with fvprintf(). Small and medium sized writings
>> on /dev/full don't trigger error and 1MB does.
>>
>> But if fprintf() is used, it returns a negative value from the very first byte written.
> I correct myself. In my test, fprintf() returned -1 for another reason (connection was already closed
> at this moment)
> However, if fvprintf(...) is followed by res=fflush(con) then res is -1
> if we try to write on /dev/full. May be we have to use this to trigger
> an error message in R.
>
> Serguei.
>
>>>   The regression test I put in had this problem; I'm working on MacOS and Windows, so I never got to actually try it before committing.
>>>
>>> Unfortunately, it doesn't look possible to catch the final flush of the buffer when the connection is closed, so small writes won't trigger any error.
>>>
>>> It's also possible that whatever system you're on doesn't signal an error when the write fails.
>>>
>>> Duncan Murdoch
>>>
>>>> Cheers,
>>>>
>>>> j.
>>>>
>>>>
>>>> On 4 July 2017 at 21:37, Duncan Murdoch <murdoch.duncan at gmail.com
>>>> <mailto:murdoch.duncan at gmail.com>> wrote:
>>>>
>>>>     On 04/07/2017 11:50 AM, Jean-S?bastien Bevilacqua wrote:
>>>>
>>>>         Hello,
>>>>         You can find here a patch to fix disk corruption.
>>>>         When your disk is full, the write function exit without error
>>>>         but the file
>>>>         is truncated.
>>>>
>>>> https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17243
>>>> <https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17243>
>>>>
>>>>
>>>>     Thanks.  I didn't see that when it came through (or did and forgot).
>>>>     I'll probably move the error check to a lower level (in the
>>>>     Rconn_printf function), if tests show that works.
>>>>
>>>>     Duncan Murdoch
>>>>
>>>>
>>>>     ______________________________________________
>>>>     R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>>>>     https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>     <https://stat.ethz.ch/mailman/listinfo/r-devel>
>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> -------- January Weiner --------------------------------------
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>

-- 
Serguei Sokol
Ingenieur de recherche INRA
Metabolisme Integre et Dynamique des Systemes Metaboliques (MetaSys)

LISBP, INSA/INRA UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04

tel: +33 5 6155 9276
fax: +33 5 6704 8825
email: sokol at insa-toulouse.fr
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http://www.lisbp.fr

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[Rd] [New Patch] Fix disk corruption when writing
Serguei Sokol