[Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
peter dalgaard
pdalgd at gmail.com
Fri Jan 1 23:48:09 CET 2016
Nice catch you two!!!
Happy New Year
-pd
> 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
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
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>
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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