From aixtools at gmail.com  Fri Dec 18 14:21:43 2015
From: aixtools at gmail.com (Michael Felt)
Date: Fri, 18 Dec 2015 14:21:43 +0100
Subject: [Rd] Assistance much appreciated
In-Reply-To: <DCB5B35F-85DD-4078-8F02-940C368DCE95@r-project.org>
References: <5672EA93.104@gmail.com>
	<DCB5B35F-85DD-4078-8F02-940C368DCE95@r-project.org>
Message-ID: <56740867.9000906@gmail.com>

On 2015-12-18 02:29, Simon Urbanek wrote:
> Michael,
>
> I got access to PDP AIX so I can try to replicate your problem. Can you, please, share exactly your setup - AIX version and well as how exactly you installed the compilers (=where from)? I can then try to replicate it. AFAICS there is no official binary for gfortran nor gcc 4.7 so it must be some 3rd party - which could also be a problem.
>
> Thanks,
> Simon
>
I installed a fresh system - AIX 6.1 TL5 this time, and built the system 
from scratch.

It is a long read, and I also made some discoveries about the contents 
of some of my newer packaging.
However, it you go through it you will see what is needed to make it all 
work.

The starting point are these filesets - available via my aixtools.net site:

root at x069:[/data/prj/cran/32/R-aix-3.2.3]ls -l /tmp/download
total 622400
-rw-r--r--    1 root     system        27482 Dec 18 12:34 .toc
-rwxrwxr--    1 199      33           828928 Sep 17 2012  
aixtools.gmp.5.0.5.0.I
-rw-r--r--    1 root     system      2102784 Jul 30 07:04 
aixtools.gnu.autoconf.2.69.0.0.aix537.I
-rw-r--r--    1 root     system      1461248 Jul 30 07:56 
aixtools.gnu.automake.1.15.0.0.aix537.I
-rw-r--r--    1 root     system      5321728 Sep 13 15:10 
aixtools.gnu.bash.4.3.42.0.aix537.I
-rw-r--r--    1 root     system     11640832 Aug 07 00:02 
aixtools.gnu.gettext.0.19.5.0.aix537.I
-rw-r--r--    1 root     system      1702912 Jul 30 08:08 
aixtools.gnu.libtool.2.4.6.0.aix537.I
-rw-r--r--    1 root     system       541184 Jun 13 2015  
aixtools.gnu.m4.1.4.17.0.aix537.I
-rw-r--r--    1 root     system      1229824 Jun 13 2015  
aixtools.gnu.make.4.1.0.0.aix537.I
-rw-r--r--    1 root     system      1348096 Nov 27 2014  
aixtools.libiconv.1.14.0.0.aix537.I
-rw-r--r--    1 199      33           265216 Oct 31 2014  
aixtools.mpc.1.0.2.0.I
-rw-r--r--    1 199      33           576512 Oct 31 2014  
aixtools.mpfr.2.4.2.0.I
-rw-r--r--    1 199      1954      290915328 Apr 16 2015  
aixtools.obj.gcc.4.7.4.0.aix537.I
-rw-r--r--    1 root     system       679424 Jun 02 2015  
aixtools.xz.5.0.8.0.aix537.I


Note: the aixtools.xz (lzma support) was a surprise, as the internal one 
did not link properly, for some reason (all in the file,
not included here, but available at: 
http://download.aixtools.net/test/R/build-freshstart.text (Trying to not 
overfill lots of mail boxes).

Also note, in the file there is a segmentation fault, core dump, but 
does not halt the build. Maybe this has been around on my previous 
builds on AIX 5.3 and 7.1 - but not noticed.

I did struggle for a few days with a buggy bos.adt.libm on AIX 7.1 
(installing an older version made my problem go away).

Segmentation error text:

  *** caught segfault ***
address 55544300, cause 'memory not mapped'

Traceback:
  1: format.POSIXlt(as.POSIXlt(x, tz), format, usetz, ...)
  2: structure(format.POSIXlt(as.POSIXlt(x, tz), format, usetz, 
...),     names = names(x))
  3: format.POSIXct(Sys.time(), "%Y-%m-%d at %H:%M:%S")
  4: format(Sys.time(), "%Y-%m-%d at %H:%M:%S")
  5: eval(expr, envir, enclos)
  6: eval(expr, env)
  7: withVisible(eval(expr, env))
  8: doTryCatch(return(expr), name, parentenv, handler)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(withVisible(eval(expr, env)), error = function(e) e)
12: evalWithOpt(ce, options, env)
13: processRdChunk(block, stage, options, env, macros = macros)
14: recurse(block[[i]])
15: recurse(block[[i]])
16: recurse(block[[i]])
17: recurse(block)
18: getDynamicFlags(block)
19: recurse(block)
20: expandDynamicFlags(recurse(block), options)
21: processRdSexprs(Rd, stage, options, macros = attr(Rd, "macros"))
22: prepare_Rd(f, encoding = encoding, defines = os, stages = 
stages,     warningCalls = FALSE, stage2 = step > 1L, stage3 = step 
 >         2L, macros = macros)
23: FUN(X[[i]], ...)
24: lapply(files, .fetch_Rd_object)
25: .build_Rd_db(dir, manfiles, db_file = db_file, encoding = 
encoding,     built_file = built_file)
26: 
tools:::.install_package_Rd_objects("/data/prj/cran/R-3.2.3/src/library/tools",     
"../../library/tools")
aborting ...
/bin/sh[3]: 4915208 Segmentation fault(coredump)
Makefile:73: recipe for target 'tools.Rdts' failed
make[3]: *** [tools.Rdts] Error 1
make[3]: Leaving directory '/data/prj/cran/32/R-aix-3.2.3/src/library'
Makefile:79: recipe for target 'Rdobjects' failed
make[2]: *** [Rdobjects] Error 2
make[2]: Leaving directory '/data/prj/cran/32/R-aix-3.2.3/src/library'
Makefile:62: recipe for target 'docs' failed
make[1]: *** [docs] Error 2
make[1]: Leaving directory '/data/prj/cran/32/R-aix-3.2.3/src/library'
Makefile:72: recipe for target 'docs' failed
make: [docs] Error 2 (ignored)
make[1]: Entering directory 
'/data/prj/cran/32/R-aix-3.2.3/src/library/Recommended'
make[2]: Entering directory 
'/data/prj/cran/32/R-aix-3.2.3/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
....

Simon - Thanks again for testing/checking,
Michael



[Rd] Assistance much appreciated
Michael Felt