Re: [Rd] Assistance much appreciated
On 2015-12-17 21:37, peter dalgaard wrote:
As you're dying in an else clause, a previous if () must contain the clue.
Unfortunately not necessarily the matching one.
My guess is that your TRE library is broken. The line should have matched the RE
"regline" defined as
tre_regcomp(®line, "^[^:]+:[[:blank:]]*", REG_EXTENDED);
...and used here:
if(tre_regexecb(®line, line, 1, regmatch, 0) == 0) {
but apparently does not.
int
tre_regcomp(regex_t *preg, const char *regex, int cflags)
{
return tre_regncomp(preg, regex, regex ? strlen(regex) : 0, cflags);
}
The code is a bit too 'string busy' for me to be comfortable - so I took
a different approach to look for potential differences in how 32-bit
versus 64-bit were viewing things. Again, it may not be that the root
cause is here - but I hope looking at the diff -u of the .i files gives
someone an good impression of how the data types are being swapped about.
For one example - I had a very old program that had a typedef for
"typedef unsigned long long ulonglong_t;" that would not parse well.
When I changed that to unit64_t (as defined in /usr/include/sys/stdint.h)
#ifndef _STD_UINT64_T
#ifdef __64BIT__
typedef unsigned long uint64_t;
#else /* _ILP32 */
#if defined(_LONG_LONG)
typedef unsigned long long uint64_t;
#endif
#endif
#endif /* _STD_UINT64_T */
All my compilers and os mix (gcc, xlc, AIX and linux) were happy!
So, I am hoping something triggers a thought in the following: (or the
haystack gets smaller...)
root@x072:[/]diff -u /data/prj/cran/??/R-3.2.3/src/extra/tre/regcomp.i
--- /data/prj/cran/32/R-3.2.3/src/extra/tre/regcomp.i 2015-12-18
08:10:25.0 +
+++ /data/prj/cran/64/R-3.2.3/src/extra/tre/regcomp.i 2015-12-18
08:10:58.0 +
@@ -1,5 +1,5 @@
# 1 "/data/prj/cran/R-3.2.3/src/extra/tre/regcomp.c"
- # 1 "/data/prj/cran/32/R-3.2.3/src/extra/tre//"
+ # 1 "/data/prj/cran/64/R-3.2.3/src/extra/tre//"
# 1 ""
# 1 "/data/prj/cran/R-3.2.3/src/extra/tre/regcomp.c"
# 10 "/data/prj/cran/R-3.2.3/src/extra/tre/regcomp.c"
@@ -171,18 +171,11 @@
typedef long int ptrdiff_t;
# 119
"/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/include-fixed/sys/types.h" 3 4
typedef unsigned int wctype_t;
+ # 128
"/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/include-fixed/sys/types.h" 3 4
+ typedef long fpos_t;
-
-
-
- typedef long long fpos_t;
-
-
-
-
-
typedef long long fpos64_t;
# 145
"/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/include-fixed/sys/types.h" 3 4
typedef int time_t;
@@ -258,9 +251,9 @@
- typedef long long off_t;
+ typedef long off_t;
@@ -2785,8 +2778,8 @@
extern char *tmpnam(char *);
extern int fclose(FILE *);
extern int fflush(FILE *);
- extern FILE * fopen64(const char *restrict, const char *restrict);
- extern FILE * freopen64(const char *restrict, const char *restrict,
FILE *restrict);
+ extern FILE * fopen(const char *restrict, const char *restrict);
+ extern FILE * freopen(const char *restrict, const char *restrict, FILE
*restrict);
extern void setbuf(FILE *restrict, char *restrict);
extern int setvbuf(FILE *restrict, char *restrict, int, size_t);
extern int fprintf(FILE *restrict, const char *restrict, ...);
@@ -2816,9 +2809,9 @@
extern char *gets(char *);
extern int puts(const char *);
extern int ungetc(int, FILE *);
- extern int fgetpos64(FILE *restrict, fpos_t *restrict);
+ extern int fgetpos(FILE *restrict, fpos_t *restrict);
extern int fseek(FILE *, long int, int);
- extern int fsetpos64(FILE *, const fpos_t *);
+ extern int fsetpos(FILE *, const fpos_t *);
extern long ftell(FILE *);
extern void rewind(FILE *);
extern void perror(const char *);
@@ -2841,8 +2834,8 @@
extern void flockfile(FILE *);
extern void funlockfile(FILE *);
- extern int fseeko64(FILE *, off_t, int);
- extern off_t ftello64(FILE *);
+ extern int fseeko(FILE *, off_t, int);
+ extern off_t ftello(FILE *);
extern int ftrylockfile(FILE *);
extern void funlockfile(FILE *);
# 470
"/opt/lib/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/include-fixed/stdio.h" 3 4
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Re: [Rd] Assistance much appreciated
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 built gcc and gfortran myself. Available via http://download.aixtools.net/test/aixtools.obj.gcc.4.7.4.0.aix537.I (still in the test directory because the fileset name should be aixtools.gnu.gcc) - other filesets and instructions are available at: http://download.aixtools.net/gnu/gcc/ Note, especially, I was not smart enough - then - to automatically run the mkheaders command (full command is either /opt/libexec/gcc/powerpc-ibm-aix5.3.7.0/4.7.4/install-tools/mkheaders or /opt/libexec/gcc/powerpc-ibm-aix5.3.0.0/4.7.4/install-tools/mkheaders depending on the version of libtool I had installed when packaging (the latest also looks at the TL level, hence 5.3.7.0 rather that 5.3.0.0) Only looking at the rte (runtime) filesets - this is what I have added: All are available via http:://www.aixtools.net (wiki interface) or http://download.aixtools.net (self-service). The AIXTOOLBOX approach uses rpm for packaging - which I did not understand when I got started several years back. And I am not switching to rpm - following in the footsteps of Perzl because: a) Michael Perzl does an excellent job of keeping the AIXTOOLBOX where it should be - no need to replicate that b) I hate the RPM dependency nightmare (e.g., installing three rpm -dev packages just to get 5 include files) c) The RPM.spec files often (well occaisionally, but once is once too many for me) overwrite AIX/IBM installp files - so updates of one damage the other d) RPM and NIM did not work as well as NIM and INSTALLP Almost end of soapbox --- In AIX 5.2 IBM included a tool called mkinstallp. I have a tool around that - that I call buildaix - that largely automates packaging OSS/FOSS, especially when the packaging follows GNU build guidelines. root@x065:[/data/prj/cran/R-3.2.3/src/extra/tre] aixtools | grep rte < aixtools.32.R.rte 3.1.3.0C F1548 1130 1457 aixtools.bison.rte 3.0.4.0C Fbison 1504 0125 1445 aixtools.buildaix.rte 2.0.3.1C F1540 1007 2004 aixtools.bzip2.rte 1.0.6.0C F1543 1030 1351 aixtools.curl.rte 7.45.0.0C F1544 1106 1841 aixtools.gmp.rte 5.0.5.0C Fgmp version 5.0.5 for powerpc aixtools.gnu.bash.rte 4.3.42.0C F1537 0913 1505 aixtools.gnu.gettext.rte 0.19.5.0C F1531 0807 aixtools.gnu.gzip.rte 1.6.0.0C F1550 1216 1405 aixtools.gnu.gzip.rte.64 1.6.0.0C F1550 1216 1417 aixtools.gnu.m4.rte 1.4.17.0C F1523 0613 1221 aixtools.gnu.make.rte 4.1.0.0C F1523 0613 1158 aixtools.libiconv.rte 1.14.0.0C Flibiconv 1447 1127 1728 aixtools.libjpeg.rte 6.2.0.0C Flibjpeg version 6.2.0 for aixtools.libpng.rte 1.5.12.0C Flibpng version 1.5.12 for aixtools.mpc.rte 1.0.2.0C Fmpc 2014.Oct.31 15.44 CUT aixtools.mpfr.rte 2.4.2.0C Fmpfr 2014.Oct.31 15.19 CUT aixtools.obj.gcc.rte 4.7.4.0C F1515 0416 2134 aixtools.pcre.rte 8.37.0.0C F1544 1106 1445 aixtools.pkgconfig.gcc.rte aixtools.tiff.rte 4.0.6.0C F1542 1024 2144 aixtools.xz.rte5.0.8.0C F1522 0602 0809 aixtools.zlib.rte 1.2.8.1C Fzlib 1505 0203 1627 In closing, I made the mistake of thinking people know installp as well as they know rpm (at command-line). If you do not know installp at the command line level a) run rm -f /where/you/download/to/.toc after everytime you add a file b) use "smit install" to install filesets If you are comfortable with installp cli interface the standard commands to remember are: a) inutoc /where/you/download/to b) installp -d /where/you/download/to -L # to list filesets c) installp -d /where/you/download/to -agX | "all" Part II a) I download R-project files to /data/prj/cran/downloads b) cd /data/prj/cran gzip -dc downloads/R-3.2.3.tar.gz | tar xf - cp -rp R-3.2.3 R-3.2.3.dist c) ls -l 32/*.env 64/*.env sdiff -w ??/aix.env cat bin/my_shared.ksh d) slibclean; rm -rf 32/R-3.2.3; rm -rf 64/R-3.2.3 mkdir 32/R-3.2.3 mkdir 64/R-3.2.3 e) note current diffs between R-3.2.3 and R-3.2.3.dist root@x072:[/data/prj/cran]diff -ru R-3.2.3.dist R-3.2.3 diff -ru R-3.2.3.dist/configure R-3.2.3/configure --- R-3.2.3.dist/configure 2015-12-02 23:16:46.0 + +++ R-3.2.3/configure 2015-12-16 10:52:15.0 + @@ -26339,11 +26339,11 @@ ##ADD: Howe
Re: [Rd] Assistance much appreciated
On 2015-12-18 10:58, Michael Felt wrote:
c) ls -l 32/*.env 64/*.env
sdiff -w ??/aix.env
cat bin/my_shared.ksh
Forgot this part:
2015-12-18 10:00 32 and 64 bit aix
environments Page 1
export OBJECT_MODE=32export OBJECT_MODE=64
export CC="gcc -maix32 -mcpu=power5" export AR="ar -X64"
export CXX="g++ -maix32 -mcpu=power5"export CC="gcc -maix64
-mcpu=power5"
export F77="gfortran -maix32 -mcpu=power5" export CXX="g++ -maix64
-mcpu=power5"
export FC="gfortran -maix32 -mcpu=power5"export F77="gfortran
-maix64 -mcpu=power5"
export LDFLAGS="-L/opt/lib" export FC="gfortran -maix64
-mcpu=power5"
export LDFLAGS="-L/opt/lib"
2015-12-16 11:26bin/my_shared.ksh Page 1
#!/usr/bin/ksh
# my_config_test
# --with-cairo=no --with-libpng=no --with-jpeglib=no
--with-libtiff=no \
# --with-cairo=no --with-libpng=yes --with-jpeglib=yes
--with-libtiff=yes \
# --with-libpth-prefix=/opt \
# --with-aix-soname=aix
HOST=$1
RELEASE=$2
. ../${HOST}.env || exit -1
/data/prj/cran/${RELEASE}/configure --disable-lto --prefix=/opt \
--enable-R-shlib \
--with-cairo=no --with-libpng=no --with-jpeglib=no
--with-libtiff=no \
--with-readline=no --with-x=no
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Re: [Rd] Assistance much appreciated
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@x069:[/data/prj/cran/32/R-aix-3.2.3]ls -l /tmp/download
total 622400
-rw-r--r--1 root system27482 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' ...
*
Re: [Rd] Assistance much appreciated
On 2015-12-18 14:21, Michael Felt wrote: root@x069:[/data/prj/cran/32/R-aix-3.2.3]ls -l /tmp/download total 622400 -rw-r--r--1 root system27482 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 To simplify this, I put this is a compressed archive at: http://download.aixtools.net/test/R/download-aixtools.tar.bz2 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
