On 2016-01-03 17:28, Michael Felt wrote:
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 -pdI 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 referencedfrom module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), but a runtime definitionof 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 definitionof the symbol was not found. rtld: 0712-001 Symbol _gfortran_concat_string was referencedfrom module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), but a runtime definitionof 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 haltedMy 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
FYI: Still running into problems in grDevices using
/data/prj/cran/${RELEASE}/configure --disable-lto --prefix=/opt \
--disable-R-shlib --enable-R-static-lib \
--with-cairo=no --with-libpng=no --with-jpeglib=no
--with-libtiff=no \
--with-readline=no --with-x=no
So, Simon - very interested in your environment and whether make
completes successfully - to the end.
p.s. - I am a bit surprised about the messages below (line 4) because I am assuming that shared libraries are not being used (with --disable-R-shlib --enable-R-static-lib ). fyi - from memory - but my expectation is that it has to do with the -bexpall and an incorrect library search path being inserted. The symbol is in /opt/lib/ppc64 archives:
root@x069:[/opt/lib/ppc64]nm -X64 -Ae *.a | grep __register_frame_info_table libgcc_s.a[shr.o]: .__register_frame_info_table T 268466492 116libgcc_s.a[shr.o]: .__register_frame_info_table_bases T 268466364 120
libgcc_s.a[shr.o]: __register_frame_info_table D 536877472 libgcc_s.a[shr.o]: __register_frame_info_table d 536877472 24 libgcc_s.a[shr.o]: __register_frame_info_table_bases D 536880832libgcc_s.a[shr.o]: __register_frame_info_table_bases d 536880832 24
libstdc++.a[libstdc++.so.6]: .__register_frame_info_table T 269107692libstdc++.a[libstdc++.so.6]: .__register_frame_info_table t 269107692 40
libstdc++.a[libstdc++.so.6]: __register_frame_info_table U -libstdc++.a[libstdc++.so.6]: __register_frame_info_table d 537156720 8
But these are not being found, rather specified. Somehow the default behavior of gcc (i.e., the flags it passes to ld are being overruled). It will take time, but I shall find them.
make[4]: Entering directory '/data/prj/cran/64/R-aix-3.2.3/src/library/grDevices'
byte-compiling package 'grDevices' *** caught segfault *** address 6c20776173206e6f, cause 'memory not mapped' Traceback: 1: `$<-`(`*tmp*`, "name", value = "muffleWarning") 2: makeRestartList(...)3: withRestarts({ .Internal(.signalCondition(simpleWarning(msg, call), msg, call)) .Internal(.dfltWarn(msg, call))}, muffleWarning = function() NULL) 4: .signalSimpleWarning("unable to load shared object '/data/prj/cran/64/R-aix-3.2.3/modules//lapack.so':\n rtld: 0712-001 Symbol __register_frame_info_table was referenced\n from module /data/prj/cran/64/R-aix-3.2.3/modules/ /lapack.so(), but a runtime definition\n\t of the symbol was not found.\nrtld: 0712-001 Symbol __deregister_frame _info was referenced\n from module /data/prj/cran/64/R-aix-3.2.3/modules//lapack.so(), but a runtime definition \n\t of the symbol was not found.\nrtld: 0712-001 Symbol __register_frame_info_table was referenced\n from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), but a runtime definition\n\t of the symbol was not found.\nrtld: 0712-001 Symbol __deregister_frame_info was referenced\n from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), but a runtime definition\n\t of the symbol was not found.\nrtld: 0712-001 Symbol _gfortran_pow_i4_i4 was referenced\n from module /data/prj/cran/64/R-aix-3.2.3/lib/libRlapack.so(), but a runtime definition", quote(solve.default(rgb)))
5: solve.default(rgb) 6: solve(rgb) 7: drop(whitexyz %*% solve(rgb))8: make.rgb(red = c(0.625, 0.34), green = c(0.28, 0.595), blue = c(0.155, 0.07), gamma = 1.8, white = "D65", name = "Apple RGB")
9: eval(expr, envir, enclos) 10: eval(exprs[i], envir) 11: sys.source(codeFile, env, keep.source = keep.source) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers)15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n") [[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <-14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
16: try(sys.source(codeFile, env, keep.source = keep.source)) 17: loadNamespace(package, lib.loc, keep.source, partial = TRUE)18: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage")) 19: suppressPackageStartupMessages(loadNamespace(package, lib.loc, keep.source, partial = TRUE)) 20: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, compress = compress)
21: tools:::makeLazyLoading("grDevices")
aborting ...
/data/prj/cran/R-3.2.3.1/share/make/lazycomp.mk:7: recipe for target
'../../../library/grDevices/R/grDevices.rdb' failed
make[4]: *** [../../../library/grDevices/R/grDevices.rdb] Segmentation
fault (core dumped)
make[4]: Leaving directory
'/data/prj/cran/64/R-aix-3.2.3/src/library/grDevices'
Makefile:24: recipe for target 'all' failed make[3]: *** [all] Error 2make[3]: Leaving directory '/data/prj/cran/64/R-aix-3.2.3/src/library/grDevices'
Makefile:36: recipe for target 'R' failed make[2]: *** [R] Error 1 make[2]: Leaving directory '/data/prj/cran/64/R-aix-3.2.3/src/library' Makefile:28: recipe for target 'R' failed make[1]: *** [R] Error 1 make[1]: Leaving directory '/data/prj/cran/64/R-aix-3.2.3/src' Makefile:60: recipe for target 'R' failed make: *** [R] Error 1 root@x065:[/data/prj/cran/64/R-aix-3.2.3]
Thanks for looking - and finding!!! MichaelOn 01 Jan 2016, at 22:06 , Simon Urbanek<simon.urba...@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, SimonOn Jan 1, 2016, at 12:20 PM, Simon Urbanek<simon.urba...@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, SimonOn Dec 31, 2015, at 10:14 AM, Michael Felt<aixto...@gmail.com> wrote:On 2015-12-30 09:58, Michael Felt wrote:One day further - looks like tre_compile (or just before, after all).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 sysdatahttp://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 sysdataAttached 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@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 totalroot@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:0Hope this brings us (or me), closer to a resolution to an old concern.And, best wishes for the new year! MichaelStill 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@x069:[/data/prj/cran/32/R-aix-3.2.3/src/library/tools]make -s sysdata | root@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 110cc3310/0:45: /00000 | 3037fc18/0:3 3037fb88/0:4 | init> 110cc3310found 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 110cc54d0With 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@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@x069:[/data/prj/cran/64/R-aix-3.2.3/src/library/tools]make sysdatainstalling '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 4It 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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