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kleiweg@let.rug.nl

2000-Dec-22 04:10 UTC

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

The last line gets duplicated when a file is read like this:

    a <- scan(file=filename, what="", sep="\n",
                    strip.white=c(TRUE), quiet=TRUE)

(This error does not occur on Linux, the only other platform I
 tested.)

Version:
 platform = hppa2.0-hp-hpux10.20
 arch = hppa2.0
 os = hpux10.20
 system = hppa2.0, hpux10.20

Actually, all binaries are PA-RISC1.1

 status  major = 1
 minor = 2.0
 year = 2000
 month = 12
 day = 15
 language = R

Search Path:
 .GlobalEnv, package:mva, package:ctest, Autoloads, package:base
 
-- 
Peter Kleiweg
http://www.let.rug.nl/~kleiweg/


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ripley@stats.ox.ac.uk

2000-Dec-22 07:34 UTC

head link

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

This bug PR#672, also reported from your institution.  It has only been
reported from HP-UX, and only from your systems.  Could someone there debug
it, please?

On Fri, 22 Dec 2000 kleiweg@let.rug.nl wrote:
> 
> The last line gets duplicated when a file is read like this:
> 
>     a <- scan(file=filename, what="", sep="\n",
>                     strip.white=c(TRUE), quiet=TRUE)
> 
> (This error does not occur on Linux, the only other platform I
>  tested.)
> 
> Version:
>  platform = hppa2.0-hp-hpux10.20
>  arch = hppa2.0
>  os = hpux10.20
>  system = hppa2.0, hpux10.20
> 
> Actually, all binaries are PA-RISC1.1
> 
>  status >  major = 1
>  minor = 2.0
>  year = 2000
>  month = 12
>  day = 15
>  language = R
> 
> Search Path:
>  .GlobalEnv, package:mva, package:ctest, Autoloads, package:base
>  
> -- 
> Peter Kleiweg
> http://www.let.rug.nl/~kleiweg/
> 
> 
>
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> r-devel mailing list -- Read
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>
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> 
-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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kleiweg@let.rug.nl

2000-Dec-22 12:12 UTC

head link

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

> On Fri, 22 Dec 2000 kleiweg@let.rug.nl wrote:
> > The last line gets duplicated when a file is read like this:
> > 
> >     a <- scan(file=filename, what="", sep="\n",
> >                     strip.white=c(TRUE), quiet=TRUE)
> > Version:
> >  platform = hppa2.0-hp-hpux10.20
> >  major = 1
> >  minor = 2.0
> >  year = 2000
> >  month = 12
> >  day = 15
Prof Brian D Ripley wrote:
> This bug PR#672, also reported from your institution.
That would be me. I reported this bug before, for R version
1.1.0
> It has only been reported from HP-UX, and only from your
> systems. Could someone there debug it, please?
I would fix it, if I new how to. Perhaps you can suggest
something from the warning messages I get.

During compiling I get a lot of warning messages. These are for
scan.c:

	cc -I. -I../../src/include -I../../src/include
  -I/opt_local/opt/readline/include I/opt_local/opt/tk/include
  --I/opt_local/opt/tcl/include I/opt_local/opt/jpeg6/include
  -I/opt_local/opt/png/include I/opt_local/opt/ncurses/include
  -I/opt_local/opt/zlib/include I/users1/kleiweg/R-1.2.0-source
  --DHAVE_CONFIG_H D_HPUX_SOURCE +DA1.1 +DS1.1 -Wp,-H16000
  -I/opt_local/opt/readline/include I/opt_local/opt/tk/include
  --I/opt_local/opt/tcl/include I/opt_local/opt/jpeg6/include
  -I/opt_local/opt/png/include I/opt_local/opt/ncurses/include
  -I/opt_local/opt/zlib/include I/users1/kleiweg/R-1.2.0-source
  -L/opt_local/opt/readline/lib -L/opt_local/opt/tk/lib
  -L/opt_local/opt/tcl/lib -L/opt_local/opt/jpeg6/lib
  -L/opt_local/opt/png/lib -L/opt_local/opt/ncurses/lib
  -L/opt_local/opt/zlib/lib L/users1/kleiweg/R-1.2.0-source -Aa -c
  -scan.c -o scan.o
cc: "scan.c", line 65: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 65: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 72: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 72: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 109: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 109: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 300: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 300: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 309: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 309: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 336: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 336: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 350: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 350: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 449: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 449: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 478: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 478: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 858: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 858: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 919: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 919: warning 563: Argument #1 is not the correct
type.
cc: "scan.c", line 957: warning 604: Pointers are not
assignment-compatible.
cc: "scan.c", line 957: warning 563: Argument #1 is not the correct
type.

I get these type of warnings when compiling other sources too:
	sock.c
	sys-std.c
	connections.c
	g_alab_her.c
	../../../R/src/main/gram.y
	iosupport.c
	main.c
	plot3d.c
	saveload.c

Other warnings I get are:

cc: "loglin.c", line 236: warning 562: Redeclaration of
"collap"
  with a different storage class specifier: "collap" will have
  internal linkage.
cc: "loglin.c", line 315: warning 562: Redeclaration of
"adjust"
  with a different storage class specifier: "adjust" will have
  internal linkage.

cc: "dataentry.c", line 1309: warning 562: Redeclaration of
  "closewin" with a different storage class specifier:
"closewin"
  will have internal linkage.
cc: "dataentry.c", line 1553: warning 562: Redeclaration of
  "popupmenu" with a different storage class specifier:
  "popupmenu" will have internal linkage.
cc: "dataentry.c", line 1653: warning 562: Redeclaration of
  "popdownmenu" with a different storage class specifier:
  "popdownmenu" will have internal linkage.

cc: "fexact.c", line 315: warning 562: Redeclaration of
"f2xact"
  with a different storage class specifier: "f2xact" will have
  internal linkage.
cc: "fexact.c", line 842: warning 562: Redeclaration of
"f3xact"
  with a different storage class specifier: "f3xact" will have
  internal linkage.
cc: "fexact.c", line 1188: warning 562: Redeclaration of
  "f4xact" with a different storage class specifier:
"f4xact" will
  have internal linkage.
cc: "fexact.c", line 1413: warning 562: Redeclaration of
  "f5xact" with a different storage class specifier:
"f5xact" will
  have internal linkage.
cc: "fexact.c", line 1572: warning 562: Redeclaration of
  "f6xact" with a different storage class specifier:
"f6xact" will
  have internal linkage.
cc: "fexact.c", line 1623: warning 562: Redeclaration of
  "f7xact" with a different storage class specifier:
"f7xact" will
  have internal linkage.
cc: "fexact.c", line 1726: warning 562: Redeclaration of
  "f8xact" with a different storage class specifier:
"f8xact" will
  have internal linkage.
cc: "fexact.c", line 1770: warning 562: Redeclaration of
  "f9xact" with a different storage class specifier:
"f9xact" will
  have internal linkage.
cc: "fexact.c", line 1803: warning 562: Redeclaration of
  "f10act" with a different storage class specifier:
"f10act" will
  have internal linkage.
cc: "fexact.c", line 1871: warning 562: Redeclaration of
  "f11act" with a different storage class specifier:
"f11act" will
  have internal linkage.
cc: "fexact.c", line 1896: warning 562: Redeclaration of
  "prterr" with a different storage class specifier:
"prterr" will
  have internal linkage.
cc: "fexact.c", line 1921: warning 562: Redeclaration of
"iwork"
  with a different storage class specifier: "iwork" will have
  internal linkage.

-- 
Peter Kleiweg
http://www.let.rug.nl/~kleiweg/

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ripley@stats.ox.ac.uk

2000-Dec-22 16:53 UTC

head link

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

On Fri, 22 Dec 2000 kleiweg@let.rug.nl wrote:
> > On Fri, 22 Dec 2000 kleiweg@let.rug.nl wrote:
> 
> > > The last line gets duplicated when a file is read like this:
> > > 
> > >     a <- scan(file=filename, what="",
sep="\n",
> > >                     strip.white=c(TRUE), quiet=TRUE)
> 
> > > Version:
> > >  platform = hppa2.0-hp-hpux10.20
> 
> > >  major = 1
> > >  minor = 2.0
> > >  year = 2000
> > >  month = 12
> > >  day = 15
> 
> Prof Brian D Ripley wrote:
> 
> > This bug PR#672, also reported from your institution.
> 
> That would be me. I reported this bug before, for R version
> 1.1.0
It *is* in the BUGS list shipped with 1.2.0, so why send it in again
with no references to the earlier one?
> > It has only been reported from HP-UX, and only from your
> > systems. Could someone there debug it, please?
> 
> I would fix it, if I new how to. Perhaps you can suggest
> something from the warning messages I get.
No, but I do suggest you debug it.  That is, build a debug version and run
it under gdb, and find out why this happens.  Is it just scan?
Does read.table (which uses scan) do it?  Does readLines (which does not)?
Does it happen on all files?  Only on those with CRLF or only LF line
endings?  Only on those with incomplete last lines?

It might be a compiler bug, so perhaps you would like to try compiling
with gcc.

> During compiling I get a lot of warning messages. These are for
> scan.c:
> 
> 	cc -I. -I../../src/include -I../../src/include
>   -I/opt_local/opt/readline/include I/opt_local/opt/tk/include
>   --I/opt_local/opt/tcl/include I/opt_local/opt/jpeg6/include
>   -I/opt_local/opt/png/include I/opt_local/opt/ncurses/include
>   -I/opt_local/opt/zlib/include I/users1/kleiweg/R-1.2.0-source
>   --DHAVE_CONFIG_H D_HPUX_SOURCE +DA1.1 +DS1.1 -Wp,-H16000
>   -I/opt_local/opt/readline/include I/opt_local/opt/tk/include
>   --I/opt_local/opt/tcl/include I/opt_local/opt/jpeg6/include
>   -I/opt_local/opt/png/include I/opt_local/opt/ncurses/include
>   -I/opt_local/opt/zlib/include I/users1/kleiweg/R-1.2.0-source
>   -L/opt_local/opt/readline/lib -L/opt_local/opt/tk/lib
>   -L/opt_local/opt/tcl/lib -L/opt_local/opt/jpeg6/lib
>   -L/opt_local/opt/png/lib -L/opt_local/opt/ncurses/lib
>   -L/opt_local/opt/zlib/lib L/users1/kleiweg/R-1.2.0-source -Aa -c
>   -scan.c -o scan.o
The next are the lines of signed/unsigned char warnings that occur with
more informative messages on my platforms.  You need to look up the
numbers in your manual, as we do not have a manual for your compiler.
> cc: "scan.c", line 65: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 65: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 72: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 72: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 109: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 109: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 300: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 300: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 309: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 309: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 336: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 336: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 350: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 350: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 449: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 449: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 478: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 478: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 858: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 858: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 919: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 919: warning 563: Argument #1 is not the
correct type.
> cc: "scan.c", line 957: warning 604: Pointers are not
assignment-compatible.
> cc: "scan.c", line 957: warning 563: Argument #1 is not the
correct type.

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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kleiweg@let.rug.nl

2000-Dec-23 09:21 UTC

head link

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

Peter Kleiweg skriver...
> > > Prof Brian D Ripley wrote:
> > > > This bug PR#672, also reported from your institution.
The bug fix I mailed yesterday does fix the bug, but also
introduces a new one: requested trimming of trailing white space
doesn't happen anymore. Here is a correct patch:


*** src/main/scan.c	Sat Dec  2 19:42:25 2000
--- src/main/scan.c.new	Sat Dec 23 10:02:34 2000
***************
*** 240,246 ****
      }
   donefill:
      if (strip) {
! 	while (isspace((int)*--bufp))
  	    ;
  	bufp++;
      }
--- 240,246 ----
      }
   donefill:
      if (strip) {
! 	while (--bufp >= buffer && isspace((int)*bufp))
  	    ;
  	bufp++;
      }


-- 
Er liep twee kg



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Peter Kleiweg

2000-Dec-23 09:30 UTC

head link

[Rd] (HP-UX) scan: last line gets duplicated (PR#790)

Peter Kleiweg skriver...
> > > Prof Brian D Ripley wrote:
> > > > This bug PR#672, also reported from your institution.
The bug fix I mailed yesterday does fix the bug, but also
introduces a new one: requested trimming of trailing white space
doesn't happen anymore. Here is a correct patch:


*** src/main/scan.c	Sat Dec  2 19:42:25 2000
--- src/main/scan.c.new	Sat Dec 23 10:02:34 2000
***************
*** 240,246 ****
      }
   donefill:
      if (strip) {
! 	while (isspace((int)*--bufp))
  	    ;
  	bufp++;
      }
--- 240,246 ----
      }
   donefill:
      if (strip) {
! 	while (--bufp >= buffer && isspace((int)*bufp))
  	    ;
  	bufp++;
      }


-- 
Peter Kleiweg

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