Re: [Rd] Print bug for matrix(list(NA_complex_, ...))

From: William Dunlap <wdunlap_at_tibco.com>
Date: Wed, 03 Jun 2009 09:20:48 -0700

> From: William Dunlap
> Sent: Wednesday, June 03, 2009 8:58 AM
> To: 'Martin Maechler'; Wacek Kusnierczyk
> Cc: r-devel_at_r-project.org
> Subject: RE: [Rd] Print bug for matrix(list(NA_complex_, ...))
...
> > >> There is a bug in printing val <-
> > matrix(list(NA_complex_,NA_complex_),1).
...
> > >> Note that a large number of spaces are printed
> instead of NA.
> >
> > vQ> on ubuntu 8.04 with r 2.10.0 r48703 there is almost
> > no problem (still
> > vQ> some unnecessary spaces):
> >
> > vQ> [,1] [,2]
> > vQ> [1,] NA NA
> >
> > thank you, Waclav.
> >
> > I don't see any unnecessary space (or other CPU problems),
> > using another Linux variant (RHEL 5)
> > in the three R version
> > 2.9.0 ,
> > 2.9.0-patched (r48700)
> > 2.10.0-devel (r48700)
> >
> > Can other Windows (or ...) users confirm problems in R 2.9.0
> > (or newer) ?
>
> I just tried it on 2.9.0 on the Windows GUI (RGui.exe)
> and saw similar problems. When printing to the
> command window, with either print(val) or show(val) it took
> a very long time and put $'s at the ends of the lines
> (indicating that there was text beyond the edge of the window).
> I used sink() to put the output into a file and then print() and
> show() acted quickly. The resulting file had 119 character
> lines, consisting mainly of trailing blanks:
>
> > readLines("c:/temp/val.txt") # output of
> print(val);show(val);str(val)
> [1] " [,1]
> "
> [2] "[1,]
> "
> [3] " [,2]
> "
> [4] "[1,]
> "
> [5] " [,1]
> "
> [6] "[1,]
> "
> [7] " [,2]
> "
> [8] "[1,]
> "
> [9] "List of 2"
>
> [10] " $ : cplx NA"
>
> [11] " $ : cplx NA"
>
> [12] " - attr(*, \"dim\")= int [1:2] 1 2"
>
> > nchar(readLines("c:/temp/val.txt"))
> [1] 119 119 119 119 119 119 119 119 9 12 12 32
>
> On Linux, using yesterday's 2.9.0, valgrind shows lots
> of 'depends on uninitialized value' problems that could
> explain the Linux-Windows difference in behavior:
>
> > val<-matrix(list(NA_complex_,NA_complex_),1)
> > val
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6F7E2F: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)

Here is the traceback when it enters Rf_EncodeReal: (gdb) where
#0 Rf_EncodeReal (x=nan(0x0000007a2), w=168381312, d=0, e=0, cdec=46 '.')

    at printutils.c:160
#1 0x08099aaa in Rf_PrintValueRec (s=0x9f4a4a8, env=0x9e4cc90) at print.c:359
#2 0x0809a125 in Rf_PrintValueEnv (s=0x9f4a4a8, env=0x9e4cc90) at print.c:956
#3 0x080584cb in Rf_ReplIteration (rho=0x9e4cc90, savestack=0, browselevel=0,

    state=0xbffc7820) at main.c:261
#4 0x08058573 in R_ReplConsole (rho=0x9e4cc90, savestack=0, browselevel=0)

    at main.c:306
#5 0x08058bb9 in run_Rmainloop () at main.c:967

It looks like w has a bogus value and was probably never initialized. It is called from print.c:

    354             case CPLXSXP:
    355                 if (LENGTH(tmp) == 1) {
    356                     Rcomplex *x = COMPLEX(tmp);
    357                     formatComplex(x, 1, &wr, &dr, &er, &wi, &di,
&ei, 0);
    358                     if (ISNA(x[0].r) || ISNA(x[0].i))
    359                         snprintf(pbuf, 115, "%s",
    360                                  EncodeReal(NA_REAL, w, 0, 0,
OutDec));
    361                     else
    362                         snprintf(pbuf, 115, "%s",
EncodeComplex(x[0],
    363                         wr, dr, er, wi, di, ei, OutDec));

and I think the 'w' needs to be replaced by something reasonable for printing "NA"
(or "NA_complex_?, I don't know all of what this code is used for). Usually complex printing uses wr and wi, not w, so w is not initialized.

> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6F7E44: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6F7E4C: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6FA87A: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6F86E8: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x6F86FA: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x711183: _IO_padn (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6F8713: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> ==24859==
> ==24859== Conditional jump or move depends on uninitialised value(s)
> ==24859== at 0x7111BF: _IO_padn (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6F8713: vfprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x7177A5: vsnprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x6FF4E1: snprintf (in /lib/tls/libc-2.3.4.so)
> ==24859== by 0x809DDC1: Rf_EncodeReal (printutils.c:179)
> ==24859== by 0x8099AA9: Rf_PrintValueRec (print.c:359)
> ==24859== by 0x809A124: Rf_PrintValueEnv (print.c:956)
> ==24859== by 0x80584CA: Rf_ReplIteration (main.c:261)
> ==24859== by 0x8058572: R_ReplConsole (main.c:306)
> ==24859== by 0x8058BB8: run_Rmainloop (main.c:967)
> ==24859== by 0x8056A70: main (Rmain.c:33)
> Bill Dunlap
> TIBCO Software Inc - Spotfire Division
> wdunlap tibco.com
>
> >
> > Regards,
> > Martin Maechler
> >
> > >> Compare the
> > >> unproblematic real case:
> > >>
> > >> print(structure(list(NA_real_, NA_real_), .Dim = 1:2))
> > >> [,1] [,2]
> > >> [1,] NA NA
> > >>
> > >> Also, when printed in the read-eval-print loop,
> > printing takes a very very
> > >> long time:
> > >>
> > >>
> > >>> proc.time(); matrix(list(NA_complex_,NA_complex_),1);
> > proc.time()
> > >>>
> > >> user system elapsed
> > >> 74.35 0.09 329.45
> > >>
> > >> [,1]
> > >>
> > >> [1,]
> > >>
> > >>
> > >> [,2]
> > >>
> > >> [1,]
> > >>
> > >> user system elapsed
> > >> 92.63 0.15 347.86
> > >>
> > >> 18 seconds runtime!
> > >>
> >
> > vQ> user system elapsed
> > vQ> 0.648 0.056 155.843
> > vQ> [,1] [,2]
> > vQ> [1,] NA NA
> > vQ> user system elapsed
> > vQ> 0.648 0.056 155.843
> >
> > vQ> vQ
> >
> > vQ> ______________________________________________
> > vQ> R-devel_at_r-project.org mailing list
> > vQ> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >



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