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. 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 http://metasys.insa-toulouse.fr http://www.lisbp.fr
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 http://metasys.insa-toulouse.fr http://www.lisbp.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
http://metasys.insa-toulouse.fr
http://www.lisbp.fr
-------------- next part --------------
A non-text attachment was scrubbed...
Name: connection.patch
Type: text/x-patch
Size: 599 bytes
Desc: not available
URL:
<https://stat.ethz.ch/pipermail/r-devel/attachments/20170706/289146b1/attachment.bin>