Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Jerome BENOIT
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Hash: SHA1

Hello Vincent,

thanks for your email.

I can reproduce the issue on my laptop too,
but the upstream could not reproduce it on his virtual box.
Have you try your material on a virtual box ?

Best wishes,
Jerome

On 02/03/15 13:13, Vincent Lefevre wrote:
 Control: found -1 2.58+ds-1
 
 With the following testcase
 
 
 #!/bin/sh
 
 bibtool -V
 
 cat  input.bib EOF
 @article{key,
   AUTHOR = {Aa Bbbb, Ccc and Dd, Ee and F, Gg},
   TITLE = {Some title}
 }
 EOF
 
 rm -f out-old.bib
 while true
 do
   bibtool -q -- 'select{@article}' input.bib  out-new.bib
   [ -f out-old.bib ] || cp out-new.bib out-old.bib
   cmp out-new.bib out-old.bib || break
 done
 
 
 I can reproduce the bug on two of my machines with both unstable
 and experimental bibtool packages:
   * Laptop with 2 cores, physical access.
   * Desktop machine with 8 cores, SSH access.
 
 I need to wait for a few seconds up to several dozens of seconds
 (in the worst case, it took up to 84 seconds on my laptop).
 
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Jerome BENOIT
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Hi Again,

On 02/03/15 14:46, Vincent Lefevre wrote:
 On 2015-03-02 13:34:30 +0100, Jerome BENOIT wrote:
 I can reproduce the issue on my laptop too,
 but the upstream could not reproduce it on his virtual box.
 Have you try your material on a virtual box ?
 
 I have a virtual machine with Ubuntu 14.04, but I can't reproduce the
 bug on it (the bibtool version is not the cause, since I can reproduce
 the bug on a Debian 7.8 machine, which has the same bibtool version).
 
 Note also that I can't reproduce the bug when bibtool is run under
 valgrind (by adding valgrind in front of the bibtool line in my
 testcase) on machines where I could reproduce the bug.
 

I observed the same.

 Perhaps the code runs too slowly on the virtual machine and under
 valgrind.
 
 BTW, valgrind signals a read error:
 
 ==4060== Invalid read of size 1
 ==4060==at 0x114836: ??? (in /usr/bin/bibtool)
 ==4060==by 0x115110: ??? (in /usr/bin/bibtool)
 ==4060==by 0x10B304: ??? (in /usr/bin/bibtool)
 ==4060==by 0x10B945: ??? (in /usr/bin/bibtool)
 ==4060==by 0x109FAE: ??? (in /usr/bin/bibtool)
 ==4060==by 0x506FB44: (below main) (libc-start.c:287)
 ==4060==  Address 0x7f59f1c is 0 bytes after a block of size 60 alloc'd
 ==4060==at 0x4C28C20: malloc (vg_replace_malloc.c:296)
 ==4060==by 0x1196B6: ??? (in /usr/bin/bibtool)
 ==4060==by 0x1197E0: ??? (in /usr/bin/bibtool)
 ==4060==by 0x1135BB: ??? (in /usr/bin/bibtool)
 ==4060==by 0x113734: ??? (in /usr/bin/bibtool)
 ==4060==by 0x113DB9: ??? (in /usr/bin/bibtool)
 ==4060==by 0x10BEBB: ??? (in /usr/bin/bibtool)
 ==4060==by 0x109DE4: ??? (in /usr/bin/bibtool)
 ==4060==by 0x506FB44: (below main) (libc-start.c:287)
 

Ok. I will resubmit the bug to the upstream maintainer.
The last time I submitted it, I could not reproduce the issue.
And on my side, I could hardly trace it.

Thanks,
Jerome



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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Vincent Lefevre
On 2015-03-02 13:34:30 +0100, Jerome BENOIT wrote:
 I can reproduce the issue on my laptop too,
 but the upstream could not reproduce it on his virtual box.
 Have you try your material on a virtual box ?

I have a virtual machine with Ubuntu 14.04, but I can't reproduce the
bug on it (the bibtool version is not the cause, since I can reproduce
the bug on a Debian 7.8 machine, which has the same bibtool version).

Note also that I can't reproduce the bug when bibtool is run under
valgrind (by adding valgrind in front of the bibtool line in my
testcase) on machines where I could reproduce the bug.

Perhaps the code runs too slowly on the virtual machine and under
valgrind.

BTW, valgrind signals a read error:

==4060== Invalid read of size 1
==4060==at 0x114836: ??? (in /usr/bin/bibtool)
==4060==by 0x115110: ??? (in /usr/bin/bibtool)
==4060==by 0x10B304: ??? (in /usr/bin/bibtool)
==4060==by 0x10B945: ??? (in /usr/bin/bibtool)
==4060==by 0x109FAE: ??? (in /usr/bin/bibtool)
==4060==by 0x506FB44: (below main) (libc-start.c:287)
==4060==  Address 0x7f59f1c is 0 bytes after a block of size 60 alloc'd
==4060==at 0x4C28C20: malloc (vg_replace_malloc.c:296)
==4060==by 0x1196B6: ??? (in /usr/bin/bibtool)
==4060==by 0x1197E0: ??? (in /usr/bin/bibtool)
==4060==by 0x1135BB: ??? (in /usr/bin/bibtool)
==4060==by 0x113734: ??? (in /usr/bin/bibtool)
==4060==by 0x113DB9: ??? (in /usr/bin/bibtool)
==4060==by 0x10BEBB: ??? (in /usr/bin/bibtool)
==4060==by 0x109DE4: ??? (in /usr/bin/bibtool)
==4060==by 0x506FB44: (below main) (libc-start.c:287)

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100% accessible validated (X)HTML - Blog: https://www.vinc17.net/blog/
Work: CR INRIA - computer arithmetic / AriC project (LIP, ENS-Lyon)


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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Vincent Lefevre
On 2015-03-02 14:56:07 +0100, Jerome BENOIT wrote:
 Ok. I will resubmit the bug to the upstream maintainer.
 The last time I submitted it, I could not reproduce the issue.
 And on my side, I could hardly trace it.

This is probably easier to reproduce with the new script I posted
earlier today. Moreover I think that it is also easier on a fast
machine, possibly with several cores.

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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Jerome BENOIT
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Hello Hilmar,

thanks for reminding.

On 02/03/15 09:33, Hilmar Preuße wrote:
 found 747519 2.58
 stop
 
 On 09.05.2014 16:47, Vincent Lefevre wrote:
 Package: bibtool
 Version: 2.57+ds-1
 Severity: normal

 I randomly get errors like:
 
 *** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a 
 letter
,
 _^
 Still found in 2.58.

Please you confirm that you can observe the issue on a non virtual box.
Even better, can you check on a virtual ?

Thanks in advance,
Jerome


 
 Hilmar
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Hilmar Preuße

found 747519 2.58
stop

On 09.05.2014 16:47, Vincent Lefevre wrote:

Package: bibtool
Version: 2.57+ds-1
Severity: normal

I randomly get errors like:



*** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a letter
   ,
_^

Still found in 2.58.

Hilmar
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Vincent Lefevre
Control: found -1 2.58+ds-1

With the following testcase


#!/bin/sh

bibtool -V

cat  input.bib EOF
@article{key,
  AUTHOR = {Aa Bbbb, Ccc and Dd, Ee and F, Gg},
  TITLE = {Some title}
}
EOF

rm -f out-old.bib
while true
do
  bibtool -q -- 'select{@article}' input.bib  out-new.bib
  [ -f out-old.bib ] || cp out-new.bib out-old.bib
  cmp out-new.bib out-old.bib || break
done


I can reproduce the bug on two of my machines with both unstable
and experimental bibtool packages:
  * Laptop with 2 cores, physical access.
  * Desktop machine with 8 cores, SSH access.

I need to wait for a few seconds up to several dozens of seconds
(in the worst case, it took up to 84 seconds on my laptop).

-- 
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100% accessible validated (X)HTML - Blog: https://www.vinc17.net/blog/
Work: CR INRIA - computer arithmetic / AriC project (LIP, ENS-Lyon)


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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Hilmar Preuße

On 02.03.2015 10:19, Jerome BENOIT wrote:

Hi,


Please you confirm that you can observe the issue on a non virtual
box. Even better, can you check on a virtual ?

Sorry, I have only virtual boxes running Debian unstable. Hence this 
test run on a virtual box.


Hilmar
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2015-03-02 Thread Jerome BENOIT
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Hi Again,

On 02/03/15 11:44, Hilmar Preuße wrote:
 On 02.03.2015 10:19, Jerome BENOIT wrote:
 
 Hi,
 
 Please you confirm that you can observe the issue on a non virtual
 box. Even better, can you check on a virtual ?

 Sorry, I have only virtual boxes running Debian unstable. Hence this test run 
 on a virtual box.

interesting, because the upstream maintainer could reproduced the issue on his 
virtual box
(while I can on my non-virtual box):
can send some material that reproduce the issue ?
I am aware it is a random issue: for observing the issue on my non-virtual box 
I have to play
with statistics.

Thanks in advance,
Jerome

 
 Hilmar
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-12 Thread Vincent Lefevre
Control: retitle -1 bibtool: silent corruption / Symbol does not start with a 
letter random errors with pipe

On 2014-05-10 11:28:37 +0200, Jerome BENOIT wrote:
 Meanwhile, it appears that putting a sufficiently long
 `print.line.length' fixes the issue:
 a length of 255 for the sent material does the trick.

Thanks. It also seems to solve silent corruption I've also noticed
yesterday, but I think that's directly related.

For instance, here's what I got with bibtool:

===
--- other.bib   (revision 99)
+++ other.bib   (working copy)
@@ -382,8 +382,8 @@
 }
 
 @Unpublished{alias:ensl-00549682,
-  author   = {Alias, Christophe and Pasca, Bogdan and Plesco,
- Alexandru},
+  author   = {Alias, Christophe and Pasca, Bogdan and Plesco, Alexandru}
+ ^?,
   title= {{Automatic Generation of FPGA-Specific Pipelined
  Accelerators}},
   keywords = {High-level synthesis ; Polytope model ; Pipelined

where ^? is the DEL character (7F).

I suspect that the Symbol does not start with a letter error appears
when such a corrupt output is fed to a second bibtool invocation with
a pipe, as indeed, the DEL character is not a letter.

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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-12 Thread Jerome BENOIT
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Hash: SHA1

Hello Vincent:

thanks for your feedback.

On 12/05/14 14:43, Vincent Lefevre wrote:
 Control: retitle -1 bibtool: silent corruption / Symbol does not
 start with a letter random errors with pipe
 
 On 2014-05-10 11:28:37 +0200, Jerome BENOIT wrote:
 Meanwhile, it appears that putting a sufficiently long 
 `print.line.length' fixes the issue: a length of 255 for the sent
 material does the trick.
 
 Thanks. It also seems to solve silent corruption I've also noticed 
 yesterday, but I think that's directly related.
 


This is the workaround:
the silent corruption is the bug (which appears hard to isolate).


 For instance, here's what I got with bibtool:
 
 === 
 --- other.bib   (revision 99) +++ other.bib   (working copy) @@
 -382,8 +382,8 @@ }
 
 @Unpublished{alias:ensl-00549682, -  author   = {Alias,
 Christophe and Pasca, Bogdan and Plesco, -
 Alexandru}, +  author   = {Alias, Christophe and Pasca, Bogdan
 and Plesco, Alexandru} + ^?, title=
 {{Automatic Generation of FPGA-Specific Pipelined Accelerators}}, 
 keywords = {High-level synthesis ; Polytope model ; Pipelined
 
 where ^? is the DEL character (7F).

How can we easily see that ?


 
 I suspect that the Symbol does not start with a letter error
 appears when such a corrupt output is fed to a second bibtool
 invocation with a pipe, as indeed, the DEL character is not a
 letter.
 

It is an output issue, not a pipe one:
if the '-o' option is used in the script along with temporary files,
the issue remains. 

Best wishes,
Jerome
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-12 Thread Vincent Lefevre
On 2014-05-12 14:54:42 +0200, Jerome BENOIT wrote:
  For instance, here's what I got with bibtool:
  
  === 
  --- other.bib   (revision 99) +++ other.bib   (working copy) @@
  -382,8 +382,8 @@ }
  
  @Unpublished{alias:ensl-00549682, -  author   = {Alias,
  Christophe and Pasca, Bogdan and Plesco, -
  Alexandru}, +  author   = {Alias, Christophe and Pasca, Bogdan
  and Plesco, Alexandru} + ^?, title=
  {{Automatic Generation of FPGA-Specific Pipelined Accelerators}}, 
  keywords = {High-level synthesis ; Polytope model ; Pipelined
  
  where ^? is the DEL character (7F).
 
 How can we easily see that ?

With a large .bib file (like the one provided in the testcase),
under zsh:

$ repeat 50; do bibtool -q -- 'preserve.key.case = On' -- 
'select{@InProceedings}' all.bib | out.bib; md5sum out.bib; done
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
cad92fcb81abaa785b0beb302dd80e3a  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
cad92fcb81abaa785b0beb302dd80e3a  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib
246089a0c05153f40fdfc3349882dd2b  out.bib

One can see that 2 instances have been corrupted.

Or:

while { bibtool -q -- 'preserve.key.case = On' -- 'select{@InProceedings}' 
all.bib | out.bib; [[ `md5sum out.bib` = 246089a0c05153f40fdfc3349882dd2b* ]] 
} do ; done

then look at the out.bib file with less, and search for the DEL
character (Ctrl-V Ctrl-?). Here I get 3 of them.

It seems that when the output is corrupted, it is always in the same way.

-- 
Vincent Lefèvre vinc...@vinc17.net - Web: https://www.vinc17.net/
100% accessible validated (X)HTML - Blog: https://www.vinc17.net/blog/
Work: CR INRIA - computer arithmetic / AriC project (LIP, ENS-Lyon)


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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-10 Thread Jerome BENOIT
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Again,

the upstream maintainer is working on it.

Meanwhile, it appears that putting a sufficiently long `print.line.length' 
fixes the issue:
a length of 255 for the sent material does the trick.

Best wishes,
Jerome

On 10/05/14 00:32, Vincent Lefevre wrote:
 On 2014-05-09 19:25:33 +0200, Jerome BENOIT wrote:
 Please can you send a data file that produces the issue along with
 the command line used.
 
 I've attached an archive containing the script and the input.
 Just execute:
 
   ./extract-bib-files.sh
 
 The bug doesn't always occur, and one may need more than 10 tries.
 I've also managed to get a strace output with:
 
   strace -f -o str.out ./extract-bib-files.sh
 
 (this was more difficult to reproduce) and attached the result.
 
 Otherwise, can you say whether the bug exists with version 2.55 ?
 
 Yes, I can also reproduce the bug with version 2.55 from wheezy.
 
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-09 Thread Vincent Lefevre
Package: bibtool
Version: 2.57+ds-1
Severity: normal

I randomly get errors like:

  ,
_^
*** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a letter

  ,
_^
*** BibTool ERROR:  (line 380 in stdin): Symbol does not start with a letter

  ,
_^
*** BibTool ERROR:  (line 1236 in stdin): Symbol does not start with a letter

or:

  ,
_^
*** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a letter

  ,
_^
*** BibTool ERROR:  (line 380 in stdin): Symbol does not start with a letter

(on the same files!) and sometimes no errors, while the input files
haven't changed. BibTool seems to have problems with pipes.

-- System Information:
Debian Release: jessie/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 
'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.14-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=POSIX, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages bibtool depends on:
ii  dpkg  1.17.9
ii  libc6 2.18-5
ii  libkpathsea6  2013.20130729.30972-2+b3
ii  tex-common4.04

bibtool recommends no packages.

bibtool suggests no packages.

-- no debconf information


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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-09 Thread Jerome BENOIT
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Vincent,

thanks for your report.

Please can you send a data file that produces the issue along with the command 
line used.

Otherwise, can you say whether the bug exists with version 2.55 ?

Best wishes,
Jerome 

On 09/05/14 16:47, Vincent Lefevre wrote:
 Package: bibtool
 Version: 2.57+ds-1
 Severity: normal
 
 I randomly get errors like:
 
   ,
 _^
 *** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a letter
 
   ,
 _^
 *** BibTool ERROR:  (line 380 in stdin): Symbol does not start with a letter
 
   ,
 _^
 *** BibTool ERROR:  (line 1236 in stdin): Symbol does not start with a 
 letter
 
 or:
 
   ,
 _^
 *** BibTool ERROR:  (line 109 in stdin): Symbol does not start with a letter
 
   ,
 _^
 *** BibTool ERROR:  (line 380 in stdin): Symbol does not start with a letter
 
 (on the same files!) and sometimes no errors, while the input files
 haven't changed. BibTool seems to have problems with pipes.
 
 -- System Information:
 Debian Release: jessie/sid
   APT prefers unstable
   APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 
 'experimental')
 Architecture: amd64 (x86_64)
 Foreign Architectures: i386
 
 Kernel: Linux 3.14-1-amd64 (SMP w/8 CPU cores)
 Locale: LANG=POSIX, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
 Shell: /bin/sh linked to /bin/dash
 
 Versions of packages bibtool depends on:
 ii  dpkg  1.17.9
 ii  libc6 2.18-5
 ii  libkpathsea6  2013.20130729.30972-2+b3
 ii  tex-common4.04
 
 bibtool recommends no packages.
 
 bibtool suggests no packages.
 
 -- no debconf information
 
 
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Bug#747519: bibtool: Symbol does not start with a letter random errors with pipe

2014-05-09 Thread Jerome BENOIT
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Vincent,

thanks for your prompt reply.

I could reproduce the issue on my own Debian box.

I have just sent an email to the upstream maintainer with your material (and 
some extra).

Best wishes,
Jerome

On 10/05/14 00:32, Vincent Lefevre wrote:
 On 2014-05-09 19:25:33 +0200, Jerome BENOIT wrote:
 Please can you send a data file that produces the issue along with
 the command line used.
 
 I've attached an archive containing the script and the input.
 Just execute:
 
   ./extract-bib-files.sh
 
 The bug doesn't always occur, and one may need more than 10 tries.
 I've also managed to get a strace output with:
 
   strace -f -o str.out ./extract-bib-files.sh
 
 (this was more difficult to reproduce) and attached the result.
 
 Otherwise, can you say whether the bug exists with version 2.55 ?
 
 Yes, I can also reproduce the bug with version 2.55 from wheezy.
 
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Version: GnuPG v1.4.12 (GNU/Linux)

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