Print bug for matrix(list(NA_complex_, ...))

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

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Print bug for matrix(list(NA_complex_, ...))

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