From aixtools at gmail.com  Sun Jan  3 17:28:05 2016
From: aixtools at gmail.com (Michael Felt)
Date: Sun, 03 Jan 2016 17:28:05 +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: <56894556.3020902@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>
	<56894556.3020902@gmail.com>
Message-ID: <56894C15.9060600@gmail.com>

On 2016-01-03 16:59, Michael Felt wrote:
> 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.
>
Using the dist, plus the following change:

diff -ru R-3.2.3.dist/src/extra/tre/tre-internal.h 
R-3.2.3.1/src/extra/tre/tre-internal.h
--- R-3.2.3.dist/src/extra/tre/tre-internal.h   2014-06-13 
22:15:07.000000000 +0000
+++ R-3.2.3.1/src/extra/tre/tre-internal.h      2016-01-03 
16:08:31.000000000 +0000
@@ -47,7 +47,7 @@
   #ifdef TRE_WCHAR

   /* Wide characters. */
- typedef wint_t tre_cint_t;
+ typedef uint16_t tre_cint_t;
   #define TRE_CHAR_MAX WCHAR_MAX

   #ifdef TRE_MULTIBYTE
@@ -78,7 +78,7 @@
   #else /* !TRE_WCHAR */

   /* 8 bit characters. */
- typedef short tre_cint_t;
+ typedef uint16_t tre_cint_t;
   #define TRE_CHAR_MAX 255
   #define TRE_MB_CUR_MAX 1

@@ -118,7 +118,7 @@
   #define tre_ctype(s)   wctype(s)
   #else /* !TRE_USE_SYSTEM_WCTYPE */
   /* Define our own versions of iswctype() and wctype(). */
- typedef int (*tre_ctype_t)(tre_cint_t);
+ typedef uint16_t (*tre_ctype_t)(tre_cint_t);
   #define tre_isctype(c, type) ( (type)(c) )
   tre_ctype_t tre_ctype(const char *name);
   #endif /* !TRE_USE_SYSTEM_WCTYPE */

I get the same result as with my modified configure(.ac), namely:

make[4]: Entering directory 
'/data/prj/cran/64/R-aix-3.2.3/src/library/grDevices'
byte-compiling package 'grDevices'
Warning in solve.default(rgb) :
   unable to load shared object 
'/data/prj/cran/64/R-aix-3.2.3/modules//lapack.so':
   rtld: 0712-001 Symbol _gfortran_pow_i4_i4 was referenced
       from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), 
but a runtime definition
             of the symbol was not found.
rtld: 0712-001 Symbol 
_gfortran_compare_string/data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so 
was referenced
       from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), 
but a runtime definition
             of the symbol was not found.
rtld: 0712-001 Symbol _gfortran_concat_string was referenced
       from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), 
but a runtime definition
             of the symbol was not found.
rtld: 0712-002 fatal error: exiting.
Error in solve.default(rgb) : LAPACK routines cannot be loaded
Error: unable to load R code in package 'grDevices'
Execution halted

My expectation is that this has to do with some incorrect flags being 
passed to the linker (not getting the 64-bit libraries of the compiler). 
I have had several long discussions with an AIX gcc specialist and he 
has given me several recommendations for changes to the flags used for 
creating shared libraries. I shall continue looking into this.

I am happy it is not my configure.ac changes - and I have a few ideas on 
how to resolve in configure.ac and/or in m4 files.

MF
> 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
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"
Michael Felt