From aixtools at gmail.com  Sun Jan  3 16:59:18 2016
From: aixtools at gmail.com (Michael Felt)
Date: Sun, 03 Jan 2016 16:59:18 +0100
Subject: [Rd] R,
 AIX 64-bit builds - trying to understand root cause for message:
 "Error: Line starting 'Package: tools ...' is malformed!"
In-Reply-To: <F68557F2-67ED-4EF3-8BDF-F7981D8F38C0@gmail.com>
References: <56825A4B.7010508@gmail.com> <56839C9E.2010401@gmail.com>
	<5685466E.7000804@gmail.com>
	<4BED4A65-8EE9-49B8-8AFB-4E6CC3BB5BBF@r-project.org>
	<F92F30A1-4E5C-4312-B151-692F27013F8B@r-project.org>
	<F68557F2-67ED-4EF3-8BDF-F7981D8F38C0@gmail.com>
Message-ID: <56894556.3020902@gmail.com>

On 2016-01-01 23:48, peter dalgaard wrote:
> Nice catch you two!!!
>
> Happy New Year
> -pd
I am much happier with this great start!

Simon - which compiler)s) did you use: xlc and xlfortran, or gcc/gfortran?

I have made some changes to configure(.ac) so maybe my problems are 
self-inflicted. But would be good to know what environment you are using.

Thanks for looking - and finding!!!

Michael
>> On 01 Jan 2016, at 22:06 , Simon Urbanek<simon.urbanek at r-project.org>  wrote:
>>
>> Ok, found the problem - on platforms that support it TRE uses wint_t (from wchar.h) as its type for characters (tre_cint_t) which on AIX is *signed* int. TRE uses liberally conversions between int and tre_cint_t apparently assuming that the latter is unsigned so conversions back to int are suitable for comparisons etc. On other platforms wint_t is unsigned so it works. Manually defining tre_cint_t to unsigned int fixes the issue.
>>
>> Cheers,
>> Simon
>>
>>
>> On Jan 1, 2016, at 12:20 PM, Simon Urbanek<simon.urbanek at r-project.org>  wrote:
>>
>>> Michael,
>>>
>>> thanks, I'll have a look once my PDP VMs are up again (later today). This may be a signedness issue although it's unclear why other platforms wouldn't be affected.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>> On Dec 31, 2015, at 10:14 AM, Michael Felt<aixtools at gmail.com>  wrote:
>>>
>>>> On 2015-12-30 09:58, Michael Felt wrote:
>>>>> On 2015-12-29 11:02, Michael Felt wrote:
>>>>>> This seems to be a problem that goes back a long time - and I hope someone who understands what tre is suppossed to be doing will look at this.
>>>>>>
>>>>>> A short history of other people who have reported on this on different versions of AIX. I shall only add that I get the same results on AIX 5.3 TL7, AIX 6.1 TL9 and AIX 7.1 TL3.
>>>>>>
>>>>>> Basically, with settings that work for AIX and 32-bit - the only changes being
>>>>>> -maix32 becomes -maix64
>>>>>> and
>>>>>> export OBJECT_MODE=32 becomes export OBJECT_MODE=64
>>>>>>
>>>>>> Then to shorten the 'make' bla bla, first run just make, then
>>>>>>
>>>>>> cd src/library/tools
>>>>>> make -s sysdata
>>>>>>
>>>>>> http://article.gmane.org/gmane.comp.lang.r.devel/38817/match=package+tools+malformed
>>>>>> http://article.gmane.org/gmane.comp.lang.r.devel/36886/match=package+tools+malformed
>>>>>> http://article.gmane.org/gmane.comp.lang.r.devel/23372/match=package+tools+malformed Date: 2010-01-25 06:55:41 GMT (5 years, 48 weeks, 1 day, 20 hours and 30 minutes ago)
>>>>>>
>>>>>> To that, to get debug data, I have
>>>>>>
>>>>>> * added -DTRE_DUGUG to src/extra/tre/Makefile # ALL_CFLAGS = $(ALL_CFLAGS_LO) -DTRE_DEBUG
>>>>>> * rm src/extra/tre/tre-match-parallel.o
>>>>>> * find . -name \*.so -exec rm {} \;
>>>>>> * make
>>>>>> * cd src/library/tools
>>>>>> * make -s sysdata
>>>>>>
>>>>>> Attached are the two script files of the screen output. The 32-bit one is more verbose - and contains magically lines such as:
>>>>>> found match 3037fd14 (while "found" does not occur in the 64-bit output)
>>>>>>
>>>>>> root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]wc /tmp/sysdata.??.*
>>>>>>    4730   14123  139916 /tmp/sysdata.32.text
>>>>>>    1312    3688   40528 /tmp/sysdata.64.text
>>>>>>    6042   17811  180444 total
>>>>>>
>>>>>> root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]grep -c found /tmp/sysdata.??.*
>>>>>> /tmp/sysdata.32.text:19
>>>>>> /tmp/sysdata.64.text:0
>>>>>>
>>>>>>
>>>>>> Hope this brings us (or me), closer to a resolution to an old concern.
>>>>>>
>>>>>> And, best wishes for the new year!
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>>
>>>>> Still hoping for someones curiosity/willingness.
>>>>>
>>>>> The differences show up in the first comparision that is made (of the string "3.2.3" it seems) - 32-bit is on the left, 64-bit on the right.
>>>>>
>>>>> Script command is started on Tue Dec 29 08:39:16 UTC 2015.                     |  Script command is started on Tue Dec 29 08:39:56 UTC 2015.
>>>>> root at x069:[/data/prj/cran/32/R-aix-3.2.3/src/library/tools]make -s sysdata     |  root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]make -s sysdata
>>>>> installing 'sysdata.rda'                                                       |  installing 'sysdata.rda'
>>>>> tre_tnfa_run_parallel, input type 1                                            |  tre_tnfa_run_parallel, input type 1
>>>>> length: -1                                                                     |  length: -1
>>>>> pos:chr/code | states and tags                                                 |  pos:chr/code | states and tags
>>>>> -------------+------------------------------------------------                 |  -------------+------------------------------------------------
>>>>> init>  30380200 3038014c 30380098                                             |   init>  110cc3040 110cc2f28 110cc2e10
>>>>> match end offset = -1                                                          |  match end offset = -1
>>>>> tre_tnfa_run_parallel, input type 1                                            |  tre_tnfa_run_parallel, input type 1
>>>>> length: -1                                                                     |  length: -1
>>>>> pos:chr/code | states and tags                                                 |  pos:chr/code | states and tags
>>>>> -------------+------------------------------------------------                 |  -------------+------------------------------------------------
>>>>> init>  3037fb88                                                               |   init>  110cc3310
>>>>> 0: 3/00051 | 3037fb88/0:0                                                    |    0: 3/00051 | 110cc3310/0:0
>>>>> 1: ./00046 | 3037fb88/0:0                                                    |    1: ./00046 | 110cc3310/0:0
>>>>> init>  3037fb88                                                               |   init>  110cc3310
>>>>> 1: ./00046 | 3037fb88/0:1                                                    |    1: ./00046 | 110cc3310/0:1
>>>>> 2: 2/00050 | 3037fb88/0:1                                                    |    2: 2/00050 | 110cc3310/0:1
>>>>> assertion failed                                                               |  assertion failed
>>>>> init>  3037fb88                                                               |   init>  110cc3310
>>>>> 2: 2/00050 | 3037fc18/0:1 3037fb88/0:2                                       |    2: 2/00050 | 110cc33f0/0:1 110cc3310/0:2
>>>>> 3: ./00046 | 3037fc18/0:1 3037fb88/0:2                                       |    3: ./00046 | 110cc33f0/0:1 110cc3310/0:2
>>>>> assertion failed                           *** DIFFERENCE ***                  |   init>  110cc3310
>>>>> init>  3037fb88                                                               |    3: ./00046 | 110cc3310/0:3
>>>>> 3: ./00046 | 3037fc18/0:1 3037fb88/0:3                                       |    4: 3/00051 | 110cc3310/0:3
>>>>> 4: 3/00051 | 3037fc18/0:1 3037fb88/0:3                                       |  assertion failed
>>>>> assertion failed                                                               |   init>  110cc3310
>>>>> init>  3037fb88                                                               |    4: 3/00051 | 110cc33f0/0:3 110cc3310/0:4
>>>>> 4: 3/00051 | 3037fc18/0:3 3037fb88/0:4                                       |    5: /00000 | 110cc33f0/0:3 110cc3310/0:4
>>>>> 5: /00000 | 3037fc18/0:3 3037fb88/0:4 |   init>  110cc3310
>>>>> found match 3037fd14 *** DIFFERENCE ***                   |  match end offset = -1
>>>>> match end offset = 5 *** DIFFERENCE ***                   |  tre_tnfa_run_parallel, input type 1
>>>>> tre_tnfa_run_parallel, input type 1                                            |  length: -1
>>>>> length: -1                                                                     |  pos:chr/code | states and tags
>>>>> pos:chr/code | states and tags                                                 |  -------------+------------------------------------------------
>>>>> -------------+------------------------------------------------                 |   init>  110cc4780 110cc4668 110cc4550
>>>>> init>  303811c0 3038110c 30381058                                             |  match end offset = -1
>>>>> match end offset = -1                                                          |  tre_tnfa_run_parallel, input type 1
>>>>> tre_tnfa_run_parallel, input type 1                                            |  length: -1
>>>>> length: -1                                                                     |  pos:chr/code | states and tags
>>>>> pos:chr/code | states and tags                                                 |  -------------+------------------------------------------------
>>>>> -------------+------------------------------------------------                 |   init>  110cc5700 110cc55e8 110cc54d0
>>>>>
>>>> One day further - looks like tre_compile (or just before, after all).
>>>>
>>>> With TRE_DEBUG switched on in tre-compile.c and tre-ast.c I see (snip)
>>>>
>>>> --- /tmp/x.32   2015-12-31 15:09:44.000000000 +0000
>>>> +++ /tmp/x.64   2015-12-31 15:09:30.000000000 +0000
>>>> @@ -1,5 +1,5 @@
>>>> - Script command is started on Thu Dec 31 15:04:39 2015.
>>>> - root at x069:[/data/prj/cran/32/R-aix-3.2.3/src/library/tools]make sysdata
>>>> + Script command is started on Thu Dec 31 15:08:43 2015.
>>>> + root at x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]make sysdata
>>>> installing 'sysdata.rda'
>>>> echo "tools:::sysdata2LazyLoadDB(\"/data/prj/cran/R-3.2.3/src/library/tools/R/sysdata.rda\",\"../../../library/tools/R\")" | \
>>>>   R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave
>>>> @@ -167,7 +167,7 @@
>>>> initial: 1/1,0, assert 0
>>>> initial: 0/0, assert 0
>>>> initial: 0/0, assert 0
>>>> - final state 30370718
>>>> + final state 110cba530
>>>> tre_compile: parsing '(^|[^%])(%%)*%V'
>>>> AST:
>>>> catenation, sub 0, 0 tags
>>>> @@ -177,7 +177,7 @@
>>>>         assertions: bol
>>>>         union, sub -1, 0 tags
>>>>           literal (, $) (0, 36), pos 0, sub -1, 0 tags
>>>> -           literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
>>>> +           literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
>>>>       iteration {0, -1}, sub -1, 0 tags, greedy
>>>>         catenation, sub 2, 0 tags
>>>>           literal (%, %) (37, 37), pos 1, sub -1, 0 tags
>>>> @@ -197,7 +197,7 @@
>>>> Union
>>>> Literal 0-36
>>>> After union left
>>>> - Literal 38-65535
>>>> + Literal 38--1
>>>> After union right
>>>> After union right
>>>>   num_tags += 2
>>>> @@ -231,7 +231,7 @@
>>>>         assertions: bol
>>>>         union, sub -1, 0 tags
>>>>           literal (, $) (0, 36), pos 0, sub -1, 0 tags
>>>> -           literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
>>>> +           literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
>>>>       iteration {0, -1}, sub -1, 2 tags, greedy
>>>>         catenation, sub 2, 1 tags
>>>>           literal (%, %) (37, 37), pos 1, sub -1, 1 tags
>>>> @@ -255,7 +255,7 @@
>>>> Union
>>>> Literal 0-36
>>>> After union left
>>>> - Literal 38-65535
>>>> + Literal 38--1
>>>> After union right
>>>> After union right
>>>> tre_add_tag_right: tag 3
>>>> @@ -342,7 +342,7 @@
>>>>           catenation, sub -1, 0 tags
>>>>             union, sub -1, 0 tags
>>>>               literal (, $) (0, 36), pos 0, sub -1, 0 tags
>>>> -               literal (&, M-^?) (38, 65535), pos 0, sub -1, 0 tags
>>>> +               literal (&, M-^?) (38, -1), pos 0, sub -1, 0 tags
>>>>             tag 4
>>>>
>>>> It seems in 32-bit mode -1 is unsigned (65535) but -1 == -1 in 64-bit mode.
>>>>
>>>> I suspect I will "find it" - but a proposed change is appreciated.
>>>>
>>>> Happy New Year,
>>>> Michael
>>>>
>>>> ______________________________________________
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>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>> ______________________________________________
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>>>
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[Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
Michael Felt