I have been struggling with this error message - and think I finally
understand it's context.
Start
Line by line debugging shows me the function works:
...
> saveRDS(val, mapfile)
> val
$variables
$variables$IANA_HTTP_status_code_db
[1] 0 1256
$variables$IANA_URI_scheme_db
[1] 1256 3458
$variables$table_of_HTTP_status_codes
[1] 4714 830
$references
named list()
$compressed
[1] TRUE
> mapfile
[1] "./library/tools/R/sysdata.rdx"
> [1] + Stopped (SIGTSTP) R_DEFAULT_PACKAGES=NULL LC_ALL=C
./bin/R --vanilla
root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx
-rw-r--r-- 1 root 33 193 Dec 17 16:49
./library/tools/R/sysdata.rdx
root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx
?b```b`fbf" SH0#h^?<??@?Al?&_(
??(R????? ?Y?sS
C7?PG3@??j/D ?aA
OG??x??????????$??X>4?3?89#5IF?$1)'5>?
?00F??,?(dA1T?(5-?(5/![PZ\2?$?<root at x065:[/data/prj/cran/64/R-3.2.3]
root at x065:[/data/prj/cran/64/R-3.2.3]
root at x065:[/data/prj/cran/64/R-3.2.3]gzip -dc ./library/tools/R/sysdata.rdx
X
j> names IANA_HTTP_status_code_db IANA_URI_scheme_db
table_of_HTTP_status_codes???
? variables
references
compressed?root at x065:[/data/prj/cran/64/R-3.2.3]fg
R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla
>
> e
<environment: 110dbf620>
> destDir
[1] "./library/tools/R"
> compress
[1] TRUE
> debug(tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"),
compress = compress))
Error: Line starting 'Package: tools ...' is malformed!
> tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"),
compress =
compress)
Error: Line starting 'Package: tools ...' is malformed!
>
So, at the end - my gut-feeling is that the error messages is not about
the arguments, but us related to the "tools:::foo".
Where should I look next? It goes a bit beyond me to know where in R
"tools:::foo" is being parsed.
Guessing here - but might be related to the switch from 32-bit to 64-bit
AND that PowerPC is BigEndian rather than LittleEndian? Could also be
absolutely wrong, way off base, etc. --> shoot me down!
Thanks,
Michael
More experimenting with calling commands:
> tools:::foobar()
Error: Line starting 'Package: tools ...' is malformed!
> tools::foobar()
Error: Line starting 'Package: tools ...' is malformed!
> Tools:::foobar()
Error in loadNamespace(name) : there is no package called 'Tools'
> loadNamespace(tools)
Error in loadNamespace(tools) : object 'tools' not found
> loadNamespace("tools")
Error: Line starting 'Package: tools ...' is malformed!
>
On 17-Dec-15 18:02, Michael Felt wrote:> I have been struggling with this error message - and think I finally
> understand it's context.
>
> Start
>
> Line by line debugging shows me the function works:
>
> ...
> > saveRDS(val, mapfile)
> > val
> $variables
> $variables$IANA_HTTP_status_code_db
> [1] 0 1256
>
> $variables$IANA_URI_scheme_db
> [1] 1256 3458
>
> $variables$table_of_HTTP_status_codes
> [1] 4714 830
>
>
> $references
> named list()
>
> $compressed
> [1] TRUE
>
> > mapfile
> [1] "./library/tools/R/sysdata.rdx"
> > [1] + Stopped (SIGTSTP) R_DEFAULT_PACKAGES=NULL LC_ALL=C
> ./bin/R --vanilla
> root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx
> -rw-r--r-- 1 root 33 193 Dec 17 16:49
> ./library/tools/R/sysdata.rdx
> root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx
> ?b```b`fbf" SH0#h^?<??@?Al?&_(
> ??(R????? ?Y?sS
> C7?PG3@??j/D ?aA
> OG??x??????????$??X>4?3?89#5IF?$1)'5>?
> ?00F??,?(dA1T?(5-?(5/![PZ\2?$?<root at x065:[/data/prj/cran/64/R-3.2.3]
> root at x065:[/data/prj/cran/64/R-3.2.3]
> root at x065:[/data/prj/cran/64/R-3.2.3]gzip -dc
> ./library/tools/R/sysdata.rdx
> X
> j> names IANA_HTTP_status_code_db IANA_URI_scheme_db
> table_of_HTTP_status_codes???
> ? variables
> references
> compressed?root at x065:[/data/prj/cran/64/R-3.2.3]fg
> R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla
>
> >
> > e
> <environment: 110dbf620>
> > destDir
> [1] "./library/tools/R"
> > compress
> [1] TRUE
> > debug(tools:::makeLazyLoadDB(e, file.path(destDir,
"sysdata"),
> compress = compress))
> Error: Line starting 'Package: tools ...' is malformed!
> > tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"),
compress =
> compress)
> Error: Line starting 'Package: tools ...' is malformed!
> >
>
> So, at the end - my gut-feeling is that the error messages is not
> about the arguments, but us related to the "tools:::foo".
>
> Where should I look next? It goes a bit beyond me to know where in R
> "tools:::foo" is being parsed.
> Guessing here - but might be related to the switch from 32-bit to
> 64-bit AND that PowerPC is BigEndian rather than LittleEndian? Could
> also be absolutely wrong, way off base, etc. --> shoot me down!
>
> Thanks,
> Michael
On 17/12/2015 9:06 AM, Michael Felt wrote:> More experimenting with calling commands: > > tools:::foobar() > Error: Line starting 'Package: tools ...' is malformed! > > tools::foobar() > Error: Line starting 'Package: tools ...' is malformed!These both do a loadNamespace("tools").> > Tools:::foobar() > Error in loadNamespace(name) : there is no package called 'Tools' > > loadNamespace(tools) > Error in loadNamespace(tools) : object 'tools' not foundThose are expected, and unrelated.> > loadNamespace("tools") > Error: Line starting 'Package: tools ...' is malformed!This shouldn't happen. In a previous post you listed a long list of warnings about packages not being loaded; that's likely a serious problem, but I don't know if it is the cause or a consequence of this one. Something is seriously wrong with the startup. You could try debugging setup_Rmainloop in <src/main/main.c>. to see if any warnings are being generated there. There shouldn't be any. Duncan Murdoch> > > > > On 17-Dec-15 18:02, Michael Felt wrote: >> I have been struggling with this error message - and think I finally >> understand it's context. >> >> Start >> >> Line by line debugging shows me the function works: >> >> ... >>> saveRDS(val, mapfile) >>> val >> $variables >> $variables$IANA_HTTP_status_code_db >> [1] 0 1256 >> >> $variables$IANA_URI_scheme_db >> [1] 1256 3458 >> >> $variables$table_of_HTTP_status_codes >> [1] 4714 830 >> >> >> $references >> named list() >> >> $compressed >> [1] TRUE >> >>> mapfile >> [1] "./library/tools/R/sysdata.rdx" >>> [1] + Stopped (SIGTSTP) R_DEFAULT_PACKAGES=NULL LC_ALL=C >> ./bin/R --vanilla >> root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx >> -rw-r--r-- 1 root 33 193 Dec 17 16:49 >> ./library/tools/R/sysdata.rdx >> root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx >> ?b```b`fbf" SH0#h^?<??@?Al?&_( >> ??(R????? ?Y?sS >> C7?PG3@??j/D ?aA >> OG??x??????????$??X>4?3?89#5IF?$1)'5>? >> ?00F??,?(dA1T?(5-?(5/![PZ\2?$?<root at x065:[/data/prj/cran/64/R-3.2.3] >> root at x065:[/data/prj/cran/64/R-3.2.3] >> root at x065:[/data/prj/cran/64/R-3.2.3]gzip -dc >> ./library/tools/R/sysdata.rdx >> X >> j> names IANA_HTTP_status_code_db IANA_URI_scheme_db >> table_of_HTTP_status_codes??? >> ? variables >> references >> compressed?root at x065:[/data/prj/cran/64/R-3.2.3]fg >> R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla >> >>> >>> e >> <environment: 110dbf620> >>> destDir >> [1] "./library/tools/R" >>> compress >> [1] TRUE >>> debug(tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"), >> compress = compress)) >> Error: Line starting 'Package: tools ...' is malformed! >>> tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"), compress >> compress) >> Error: Line starting 'Package: tools ...' is malformed! >>> >> >> So, at the end - my gut-feeling is that the error messages is not >> about the arguments, but us related to the "tools:::foo". >> >> Where should I look next? It goes a bit beyond me to know where in R >> "tools:::foo" is being parsed. >> Guessing here - but might be related to the switch from 32-bit to >> 64-bit AND that PowerPC is BigEndian rather than LittleEndian? Could >> also be absolutely wrong, way off base, etc. --> shoot me down! >> >> Thanks, >> Michael > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
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 On Dec 17, 2015, at 12:02 PM, Michael Felt <aixtools at gmail.com> wrote:> I have been struggling with this error message - and think I finally understand it's context. > > Start > > Line by line debugging shows me the function works: > > ... > > saveRDS(val, mapfile) > > val > $variables > $variables$IANA_HTTP_status_code_db > [1] 0 1256 > > $variables$IANA_URI_scheme_db > [1] 1256 3458 > > $variables$table_of_HTTP_status_codes > [1] 4714 830 > > > $references > named list() > > $compressed > [1] TRUE > > > mapfile > [1] "./library/tools/R/sysdata.rdx" > > [1] + Stopped (SIGTSTP) R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla > root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx > -rw-r--r-- 1 root 33 193 Dec 17 16:49 ./library/tools/R/sysdata.rdx > root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx > ?b```b`fbf" SH0#h^?<??@?Al?&_( > ??(R????? ?Y?sS > C7?PG3@??j/D ?aA OG??x??????????$??X>4?3?89#5IF?$1)'5>? > ?00F??,?(dA1T?(5-?(5/![PZ\2?$?<root at x065:[/data/prj/cran/64/R-3.2.3] > root at x065:[/data/prj/cran/64/R-3.2.3] > root at x065:[/data/prj/cran/64/R-3.2.3]gzip -dc ./library/tools/R/sysdata.rdx > X > j> names IANA_HTTP_status_code_db IANA_URI_scheme_db table_of_HTTP_status_codes??? > ? variables > references > compressed?root at x065:[/data/prj/cran/64/R-3.2.3]fg > R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla > > > > > e > <environment: 110dbf620> > > destDir > [1] "./library/tools/R" > > compress > [1] TRUE > > debug(tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"), compress = compress)) > Error: Line starting 'Package: tools ...' is malformed! > > tools:::makeLazyLoadDB(e, file.path(destDir, "sysdata"), compress = compress) > Error: Line starting 'Package: tools ...' is malformed! > > > > So, at the end - my gut-feeling is that the error messages is not about the arguments, but us related to the "tools:::foo". > > Where should I look next? It goes a bit beyond me to know where in R "tools:::foo" is being parsed. > Guessing here - but might be related to the switch from 32-bit to 64-bit AND that PowerPC is BigEndian rather than LittleEndian? Could also be absolutely wrong, way off base, etc. --> shoot me down! > > Thanks, > Michael > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
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, > SimonI 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 at x065:[/data/prj/cran/R-3.2.3/src/extra/tre] aixtools | grep rte < aixtools.32.R.rte 3.1.3.0 C F 1548 1130 1457 aixtools.bison.rte 3.0.4.0 C F bison 1504 0125 1445 aixtools.buildaix.rte 2.0.3.1 C F 1540 1007 2004 aixtools.bzip2.rte 1.0.6.0 C F 1543 1030 1351 aixtools.curl.rte 7.45.0.0 C F 1544 1106 1841 aixtools.gmp.rte 5.0.5.0 C F gmp version 5.0.5 for powerpc aixtools.gnu.bash.rte 4.3.42.0 C F 1537 0913 1505 aixtools.gnu.gettext.rte 0.19.5.0 C F 1531 0807 0000 aixtools.gnu.gzip.rte 1.6.0.0 C F 1550 1216 1405 aixtools.gnu.gzip.rte.64 1.6.0.0 C F 1550 1216 1417 aixtools.gnu.m4.rte 1.4.17.0 C F 1523 0613 1221 aixtools.gnu.make.rte 4.1.0.0 C F 1523 0613 1158 aixtools.libiconv.rte 1.14.0.0 C F libiconv 1447 1127 1728 aixtools.libjpeg.rte 6.2.0.0 C F libjpeg version 6.2.0 for aixtools.libpng.rte 1.5.12.0 C F libpng version 1.5.12 for aixtools.mpc.rte 1.0.2.0 C F mpc 2014.Oct.31 15.44 CUT aixtools.mpfr.rte 2.4.2.0 C F mpfr 2014.Oct.31 15.19 CUT aixtools.obj.gcc.rte 4.7.4.0 C F 1515 0416 2134 aixtools.pcre.rte 8.37.0.0 C F 1544 1106 1445 aixtools.pkgconfig.gcc.rte aixtools.tiff.rte 4.0.6.0 C F 1542 1024 2144 aixtools.xz.rte 5.0.8.0 C F 1522 0602 0809 aixtools.zlib.rte 1.2.8.1 C F zlib 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 <what you want to install> | "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 at 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 23:16:46.000000000 +0000 +++ R-3.2.3/configure 2015-12-16 10:52:15.000000000 +0000 @@ -26339,11 +26339,11 @@ ##ADD: However, for example, symbol in libc of memcpy is __memmove,__memmove64. ##ADD: This black magic puts lc before lR and pockets this. if test "x${OBJECT_MODE}" = "x64"; then - main_ldflags="${wl}-brtl ${wl}-bexpall ${wl}-bpT:0x100000000 ${wl}-bpD:0x110000000 -lc" + main_ldflags="${wl}-brtl ${wl}-bpT:0x100000000 ${wl}-bpD:0x110000000 -lc" else - main_ldflags="${wl}-brtl ${wl}-bexpall -lc" + main_ldflags="${wl}-brtl ${wl}-bmaxdata:0xd0000000/dsa -lc" fi - shlib_ldflags="${wl}-brtl ${wl}-G ${wl}-bexpall ${wl}-bnoentry -lc" + shlib_ldflags="${wl}-G ${wl}-bnoentry -lc" SHLIB_LIBADD="\$(LIBM)" shlib_cxxldflags="${shlib_ldflags}" if test "${GCC}" = yes; then diff -ru R-3.2.3.dist/share/make/basepkg.mk R-3.2.3/share/make/basepkg.mk --- R-3.2.3.dist/share/make/basepkg.mk 2015-03-18 23:04:12.000000000 +0000 +++ R-3.2.3/share/make/basepkg.mk 2015-12-17 12:01:02.000000000 +0000 @@ -148,7 +148,9 @@ sysdata: $(srcdir)/R/sysdata.rda @$(ECHO) "installing 'sysdata.rda'" - @$(ECHO) "tools:::sysdata2LazyLoadDB(\"$(srcdir)/R/sysdata.rda\",\"$(top_builddir)/library/$(pkg)/R\")" | \ + $(ECHO) "warnings()" | \ + R_DEFAULT_PACKAGES=NULL LC_ALL=C $(R_EXE) + $(ECHO) "tools:::sysdata2LazyLoadDB(\"$(srcdir)/R/sysdata.rda\",\"$(top_builddir)/library/$(pkg)/R\")" | \ R_DEFAULT_PACKAGES=NULL LC_ALL=C $(R_EXE) diff -ru R-3.2.3.dist/src/include/Defn.h R-3.2.3/src/include/Defn.h --- R-3.2.3.dist/src/include/Defn.h 2015-08-25 22:15:24.000000000 +0000 +++ R-3.2.3/src/include/Defn.h 2015-12-16 10:53:08.000000000 +0000 @@ -1271,7 +1271,7 @@ void invalidate_cached_recodings(void); /* from sysutils.c */ void resetICUcollator(void); /* from util.c */ void dt_invalidate_locale(); /* from Rstrptime.h */ - int R_OutputCon; /* from connections.c */ + extern int R_OutputCon; /* from connections.c */ extern int R_InitReadItemDepth, R_ReadItemDepth; /* from serialize.c */ void get_current_mem(size_t *,size_t *,size_t *); /* from memory.c */ unsigned long get_duplicate_counter(void); /* from duplicate.c */ diff -ru R-3.2.3.dist/src/library/tools/R/makeLazyLoad.R R-3.2.3/src/library/tools/R/makeLazyLoad.R --- R-3.2.3.dist/src/library/tools/R/makeLazyLoad.R 2015-08-25 22:16:54.000000000 +0000 +++ R-3.2.3/src/library/tools/R/makeLazyLoad.R 2015-12-17 06:53:34.000000000 +0000 @@ -38,9 +38,13 @@ sysdata2LazyLoadDB <- function(srcFile, destDir, compress = TRUE) { + browser() e <- new.env(hash=TRUE) + # browser() load(srcFile, e) + # browser() makeLazyLoadDB(e, file.path(destDir, "sysdata"), compress = compress) + # browser() } list_data_in_pkg <- function(package, lib.loc = NULL, dataDir = NULL) diff -ru R-3.2.3.dist/src/library/tools/src/gramLatex.c R-3.2.3/src/library/tools/src/gramLatex.c --- R-3.2.3.dist/src/library/tools/src/gramLatex.c 2015-12-09 23:20:01.000000000 +0000 +++ R-3.2.3/src/library/tools/src/gramLatex.c 2015-12-17 14:50:14.000000000 +0000 @@ -1358,7 +1358,7 @@ /* The lookahead symbol. */ - int yychar; + extern int yychar; #ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN @@ -1370,7 +1370,7 @@ #endif /* The semantic value of the lookahead symbol. */ - YYSTYPE yylval YY_INITIAL_VALUE(yyval_default); + extern YYSTYPE yylval YY_INITIAL_VALUE(yyval_default); /* Location data for the lookahead symbol. */ YYLTYPE yylloc @@ -1381,7 +1381,7 @@ /* Number of syntax errors so far. */ - int yynerrs; + extern int yynerrs; /*----------. diff -ru R-3.2.3.dist/src/library/tools/src/gramRd.c R-3.2.3/src/library/tools/src/gramRd.c --- R-3.2.3.dist/src/library/tools/src/gramRd.c 2015-12-09 23:20:01.000000000 +0000 +++ R-3.2.3/src/library/tools/src/gramRd.c 2015-12-17 14:51:19.000000000 +0000 @@ -1972,7 +1972,7 @@ /* The lookahead symbol. */ - int yychar; + extern int yychar; #ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN @@ -1984,7 +1984,7 @@ #endif /* The semantic value of the lookahead symbol. */ - YYSTYPE yylval YY_INITIAL_VALUE(yyval_default); + extern YYSTYPE yylval YY_INITIAL_VALUE(yyval_default); /* Location data for the lookahead symbol. */ YYLTYPE yylloc @@ -1995,7 +1995,7 @@ /* Number of syntax errors so far. */ - int yynerrs; + extern int yynerrs; /*----------. +++++++++ The changes in /src/library/tools/R/makeLazyLoad.R are not relevant (initial learning...) f) cd 32/R-3.2.3; ../../bin/my_shared.ksh aix R-3.2.3; export OBJECT_MODE=32; make -j4; cd - g) cd 64/R-3.2.3; ../../bin/my_shared.ksh aix R-3.2.3; export OBJECT_MODE=64; make -j4 && cd - Michael p.s. please keep me posted on any difficulties - so I can add better instructions on the wiki. p.p.s. - I am using R-3.2.3 to by-pass the removal of the src/extra packages
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