[BUGZILLA #16633] duplicate symbols in tools.so, grDevices.so, graphics.so and libR.so - where should they really be?

[MichaelChirico]

The following messages remain:

../scripts/R-devel-make.text:747:ld: 0711-224 WARNING: Duplicate symbol: Rf_yylval ../scripts/R-devel-make.text:748:ld: 0711-224 WARNING: Duplicate symbol: Rf_yychar ../scripts/R-devel-make.text:749:ld: 0711-224 WARNING: Duplicate symbol: Rf_yynerrs ../scripts/R-devel-make.text:851:ld: 0711-224 WARNING: Duplicate symbol: baseRegisterIndex ../scripts/R-devel-make.text:888:ld: 0711-224 WARNING: Duplicate symbol: .Rf_dpptr ../scripts/R-devel-make.text:889:ld: 0711-224 WARNING: Duplicate symbol: baseRegisterIndex ../scripts/R-devel-make.text:890:ld: 0711-224 WARNING: Duplicate symbol: Rf_dpptr

## ** The first three are in tools.so - I expect they are meant to 'be' here, but need direction to be sure:

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/R-devel/src/library/tools/src]grep -c yylval * | grep -v :0 gramLatex.c:20 gramLatex.y:11 gramRd.c:20 gramRd.y:11

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-shared/src/main]nm -Ae *o | grep Rf_yy gram.o: .Rf_yyparse T 30528 11420 gram.o: Rf_yychar B 56712 4 gram.o: Rf_yychar d 56604 4 gram.o: Rf_yylval B 56708 4 gram.o: Rf_yylval d 56480 4 gram.o: Rf_yynerrs B 56664 4 gram.o: Rf_yynerrs d 56600 4 gram.o: Rf_yyparse D 56180 gram.o: Rf_yyparse d 56180 12 libR.so: .Rf_yyparse T 269419804 11420 libR.so: .Rf_yyparse T 270579520 libR.so: .Rf_yyparse t 270579520 40 libR.so: Rf_yychar B 537767996 4 libR.so: Rf_yychar d 537100116 4 libR.so: Rf_yylval B 537767928 4 libR.so: Rf_yylval d 537100020 4 libR.so: Rf_yynerrs B 537767992 4 libR.so: Rf_yynerrs d 537100112 4 libR.so: Rf_yyparse D 537090136 libR.so: Rf_yyparse d 537090136 12 libR.so: Rf_yyparse d 537111476 4

## baseRegisterIndex is in libR.so, grDevices.so and graphics.so ## Rf_dpptr is in libR.so and graphics.so

## *** It seems that baseRegisterIndex is defined in a .h file...

ld: 0711-228 WARNING: Duplicate symbols were found while resolving symbols. The following duplicates were found: Symbol Source-File(Object) OR Import-File{Shared-object} ------------------------- ------------------------------------------------- baseRegisterIndex /data/prj/cran/R-devel/src/library/grDevices/src/devices.c(devices.o) Duplicate {../../../../lib/libR.so}

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-shared/src/library/grDevices/src]grep -c baseRegisterIndex /data/prj/cran/R-devel/src/library/grDevices/src/* | grep -v :0 root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-shared/src/library/grDevices/src]

# 36 "/data/prj/cran/R-devel/src/library/grDevices/src/devices.c" 2 # 1 "/data/prj/cran/R-devel/src/include/GraphicsBase.h" 1 # 27 "/data/prj/cran/R-devel/src/include/GraphicsBase.h" typedef struct { GPar dp;

GPar gp;
GPar dpSaved;

Rboolean baseDevice;

} baseSystemState;

void registerBase(void); void unregisterBase(void);

void Rf_setBaseDevice(Rboolean val, pGEDevDesc dd);

int baseRegisterIndex; # 37 "/data/prj/cran/R-devel/src/library/grDevices/src/devices.c" 2 # 53 "/data/prj/cran/R-devel/src/library/grDevices/src/devices.c"

## *** devices.o (libR.so) and base.o (graphics.so) are the proud owners of the duplicate symbols:

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-shared/src/main]nm -Ae *o | grep Rf_dpptr devices.o: .Rf_dpptr T 0 104 devices.o: Rf_dpptr D 7540 devices.o: Rf_dpptr d 7540 12 libR.so: .Rf_dpptr T 270277704 104 libR.so: .Rf_dpptr T 270562140 libR.so: .Rf_dpptr t 270562140 40 libR.so: Rf_dpptr D 537087496 libR.so: Rf_dpptr d 537087496 12 libR.so: Rf_dpptr d 537110192 4

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-shared/src/library/graphics/src]nm -Ae *o | grep Rf_dpptr base.o: .Rf_dpptr T 384 108 base.o: Rf_dpptr D 5804 base.o: Rf_dpptr d 5804 12 graphics.o: .Rf_dpptr U - graphics.so: .Rf_dpptr T 268439932 108 graphics.so: .Rf_dpptr T 268687540 graphics.so: .Rf_dpptr t 268687540 40 graphics.so: Rf_dpptr D 536903524 graphics.so: Rf_dpptr d 536903524 12 graphics.so: Rf_dpptr d 536906164 4 par.o: .Rf_dpptr U - plot.o: .Rf_dpptr U -

## **** Again, it seems that it will be found in an include file...

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/R-devel/src/library/graphics/src]grep Rf_dpptr * root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/R-devel/src/library/graphics/src]

Well, sort of:

+380 / FIXME: Make this a macro to avoid function call overhead? +381 Inline it if you really think it matters. +382 / +383 GPar gpptr(pGEDevDesc dd) { +384 if (baseRegisterIndex == -1) +385 error(_("the base graphics system is not registered")); +386 baseSystemState bss = dd->gesd[baseRegisterIndex]->systemSpecific; +387 return &(bss->gp); +388 } +389 +390 GPar dpptr(pGEDevDesc dd) { +391 if (baseRegisterIndex == -1) +392 error(_("the base graphics system is not registered")); +393 baseSystemState bss = dd->gesd[baseRegisterIndex]->systemSpecific; +394 return &(bss->dp); +395 } +396 +397 / called in GNewPlot to mark device as 'dirty' / +398 void RfsetBaseDevice(Rboolean val, pGEDevDesc dd) { +399 if (baseRegisterIndex == -1) +400 error(("the base graphics system is not registered")); +401 baseSystemState *bss = dd->gesd[baseRegisterIndex]->systemSpecific; +402 bss->baseDevice = val; +403 } "base.c" The cursor is at line 403 of 403 --100%-- .

becomes: GPar Rf_gpptr(pGEDevDesc dd) { if (baseRegisterIndex == -1) Rf_error(dgettext ("graphics", "the base graphics system is not registered")); baseSystemState bss = dd->gesd[baseRegisterIndex]->systemSpecific; return &(bss->gp); }

GPar Rf_dpptr(pGEDevDesc dd) { if (baseRegisterIndex == -1) Rf_error(dgettext ("graphics", "the base graphics system is not registered")); baseSystemState bss = dd->gesd[baseRegisterIndex]->systemSpecific; return &(bss->dp); }

void Rf_setBaseDevice(Rboolean val, pGEDevDesc dd) { if (baseRegisterIndex == -1) Rf_error(dgettext ("graphics", "the base graphics system is not registered")); baseSystemState *bss = dd->gesd[baseRegisterIndex]->systemSpecific; bss->baseDevice = val; } "base.i" The cursor is at line 6798 of 6798 --100%-- .

Your call...

And, hope this helps!

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METADATA

• Bug author - Michael Felt
• Creation time - 2015-12-15 15:12:14 UTC
• Bugzilla link
• Status - CLOSED FIXED
• Alias - None
• Component - Installation
• Version - R-devel (trunk)
• Hardware - PowerPC AIX
• Importance - P5 enhancement
• Assignee - R-core
• URL -
• Modification time - 2018-02-16 17:01 UTC

[MichaelChirico]

This is FYI - still working -

I have been doing a bit of research - comparing Linux on Power, with AIX (on Power) - same machine, just a different OS.

On linux I see:

root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:/data/prj/cran/32/R-debian/lib# cd ../src/library/tools root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:/data/prj/cran/32/R-debian/src/library/tools/src# nm -AB *o | grep Rf_yy[cln]
gramLatex.o:00000004 C Rf_yychar gramLatex.o:00000004 C Rf_yylval gramLatex.o:00000004 C Rf_yynerrs gramRd.o:00000004 C Rf_yychar gramRd.o:00000004 C Rf_yylval gramRd.o:00000004 C Rf_yynerrs tools.so:00023dbc s Rf_yychar tools.so:00023db4 s Rf_yylval tools.so:00023db8 s Rf_yynerrs

On AIX I see:

rroot@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-3.2.3/src/library/tools/src] nm -AB *o | grep Rf_yy[cln] gramLatex.o: 16648 d Rf_yychar gramLatex.o: 16728 B Rf_yychar gramLatex.o: 0 - Rf_yychar:G-1 gramLatex.o: - U Rf_yylval gramLatex.o: 16652 d Rf_yylval gramLatex.o: 16668 d Rf_yynerrs gramLatex.o: 16696 B Rf_yynerrs gramLatex.o: 0 - Rf_yynerrs:G-1 gramRd.o: 36508 d Rf_yychar gramRd.o: 36604 B Rf_yychar gramRd.o: 0 - Rf_yychar:G-1 gramRd.o: 36484 d Rf_yylval gramRd.o: 36600 B Rf_yylval gramRd.o: 0 - Rf_yylval:G495 gramRd.o: 36520 d Rf_yynerrs gramRd.o: 36568 B Rf_yynerrs gramRd.o: 0 - Rf_yynerrs:G-1 tools.so: 536875880 d Rf_yychar tools.so: 536877240 B Rf_yychar tools.so: 0 - Rf_yychar:G-1 tools.so: 0 - Rf_yychar:G-1 tools.so: 536875828 d Rf_yylval tools.so: 536877236 B Rf_yylval tools.so: 0 - Rf_yylval:G495 tools.so: 536875892 d Rf_yynerrs tools.so: 536877272 B Rf_yynerrs tools.so: 0 - Rf_yynerrs:G-1 tools.so: 0 - Rf_yynerrs:G-1 root@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>:[/data/prj/cran/32/R-3.2.3/src/library/tools/src]

Hence - it seems AIX method takes the following code quite literally:

Considering the following .i outputs:

aix/gramLatex.i:5647:extern SEXP Rf_yylval; aix/gramLatex.i:6042:int Rf_yychar; aix/gramLatex.i:6045:SEXP Rf_yylval; aix/gramLatex.i:6053:int Rf_yynerrs; aix/gramRd.i:6053:extern SEXP Rf_yylval; aix/gramRd.i:6972:int Rf_yychar; aix/gramRd.i:6975:SEXP Rf_yylval; aix/gramRd.i:6983:int Rf_yynerrs; debian/gramLatex.i:7373:extern SEXP Rf_yylval; debian/gramLatex.i:7733:int Rf_yychar; debian/gramLatex.i:7735:SEXP Rf_yylval ; debian/gramLatex.i:7746:int Rf_yynerrs; debian/gramRd.i:8682:extern SEXP Rf_yylval; debian/gramRd.i:9517:int Rf_yychar; debian/gramRd.i:9519:SEXP Rf_yylval ; debian/gramRd.i:9530:int Rf_yynerrs;

More closely: aix/gramLatex.i:5647:extern SEXP Rf_yylval; aix/gramLatex.i:6045:SEXP Rf_yylval; # seems to looking as a definition

debian/gramLatex.i:7373:extern SEXP Rf_yylval; debian/gramLatex.i:7735:SEXP Rf_yylval ; # looks global by definition

On AIX the variable is defined immedately, while on Linux that is postponed.

Michael

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METADATA

• Comment author - Michael Felt
• Timestamp - 2015-12-17 13:09:29 UTC

[MichaelChirico]

On Solaris with R version 3.2.3, it was also noticed that baseRegisterIndex was multiply defined, at least in graphics.so and libR.so, and the former was "hidden". Thus, any reference from graphics.so to baseRegisterIndex would bind to itself, whereas other references would bind to libR.so.
There are effectively (at least) two instances of this symbol being used.
Unsure whether this was intentional. Perhaps there are no references from graphics.so to baseRegisterIndex, which makes the header induced definition harmless but unnecessary and perhaps confusing. The "definition" of data items in headers with the use of "hidden" visibility can produce some hard to debug error conditions.

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METADATA

• Comment author - Rich Burridge
• Timestamp - 2016-04-09 14:39:10 UTC

[MichaelChirico]

I reported this last issue (about baseRegisterIndex) as https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17385

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METADATA

• Comment author - Jeroen Demeyer
• Timestamp - 2018-02-05 17:49:04 UTC

[MichaelChirico]

I've checked the current R-devel and all duplicate symbols reported here seem to have been addressed by now.

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METADATA

• Comment author - Tomas Kalibera
• Timestamp - 2018-02-16 17:01:20 UTC