R help - Apr 2017 - system call removes special characters from text output

Hello,

I am writing an R package, and I am using system() to call a perl script.
The output of the perl script is correct except for "[A/B]" is output
as
"AB". Can someone explain this behavior. I would like to try and fix
this.
many thanks,

Stephen Sefick

-- 
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods.  We are mammals, and have not exhausted the annoying little
problems of being mammals.

                                -K. Mullis

"A big computer, a complex algorithm and a long time does not equal
science."

                              -Robert Gentleman

	[[alternative HTML version deleted]]

Sorry, RPsychic package not found. Please install package reprex, apply it to
your problem and try again. Note that if this problem can only be produced from
within a package then there is an R-package-devel mailing list that would be a
more appropriate place to ask. Also, if the problem is actually in the perl code
or in the shell (this seems likely to me) then you probably need to look even
further afield for help.
-- 
Sent from my phone. Please excuse my brevity.

On April 3, 2017 8:57:07 PM PDT, stephen sefick <ssefick at gmail.com>
wrote:
>Hello,
>
>I am writing an R package, and I am using system() to call a perl
>script.
>The output of the perl script is correct except for "[A/B]" is
output
>as
>"AB". Can someone explain this behavior. I would like to try and
fix
>this.
>many thanks,
>
>Stephen Sefick

Hi Jeff,

My apologies for not providing enough information. The perl code works as
expected at the shell (without calling it from R). I have tried the system
call inside of an ESS R session and at a the shell. Both of these produce
the unexpected result. I can provide whatever information that is needed.
kindest regards,

Stephen

On Mon, Apr 3, 2017 at 11:23 PM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us>
wrote:
> Sorry, RPsychic package not found. Please install package reprex, apply it
> to your problem and try again. Note that if this problem can only be
> produced from within a package then there is an R-package-devel mailing
> list that would be a more appropriate place to ask. Also, if the problem is
> actually in the perl code or in the shell (this seems likely to me) then
> you probably need to look even further afield for help.
> --
> Sent from my phone. Please excuse my brevity.
>
> On April 3, 2017 8:57:07 PM PDT, stephen sefick <ssefick at
gmail.com> wrote:
> >Hello,
> >
> >I am writing an R package, and I am using system() to call a perl
> >script.
> >The output of the perl script is correct except for "[A/B]"
is output
> >as
> >"AB". Can someone explain this behavior. I would like to try
and fix
> >this.
> >many thanks,
> >
> >Stephen Sefick
>


-- 
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods.  We are mammals, and have not exhausted the annoying little
problems of being mammals.

                                -K. Mullis

"A big computer, a complex algorithm and a long time does not equal
science."

                              -Robert Gentleman

	[[alternative HTML version deleted]]

I can't reproduce this.

On my system, the contents of an executable file named tmp.pl:

#! /opt/local/bin/perl
print "[A/B]\n";

At a shell prompt:

[72]% ./tmp.pl
[A/B]

Inside R:
> system(' ./tmp.pl')
[A/B]


-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062


On 4/3/17, 8:57 PM, "R-help on behalf of stephen sefick"
<r-help-bounces at r-project.org on behalf of ssefick at gmail.com> wrote:

    Hello,
    
    I am writing an R package, and I am using system() to call a perl script.
    The output of the perl script is correct except for "[A/B]" is
output as
    "AB". Can someone explain this behavior. I would like to try and
fix this.
    many thanks,
    
    Stephen Sefick
    
    -- 
    Let's not spend our time and resources thinking about things that are so
    little or so large that all they really do for us is puff us up and make us
    feel like gods.  We are mammals, and have not exhausted the annoying little
    problems of being mammals.
    
                                    -K. Mullis
    
    "A big computer, a complex algorithm and a long time does not equal
    science."
    
                                  -Robert Gentleman
    
    	[[alternative HTML version deleted]]
    
    ______________________________________________
    R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.

Don,

Thank you for your reply. I found no problems in the perl script, but I
found that I had inadvertently swapped file names in my call to system("
script.pl file1 file2") works as expected system(script.pl file2 file1)
produces the output that formed my original query.

Thanks so much, and I learned to not code after 10 PM.
kindest regards,

Stephen

On Wed, Apr 5, 2017 at 4:06 PM, MacQueen, Don <macqueen1 at llnl.gov>
wrote:
> I can't reproduce this.
>
> On my system, the contents of an executable file named tmp.pl:
>
> #! /opt/local/bin/perl
> print "[A/B]\n";
>
> At a shell prompt:
>
> [72]% ./tmp.pl
> [A/B]
>
> Inside R:
>
> > system(' ./tmp.pl')
> [A/B]
>
>
> --
> Don MacQueen
>
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
>
>
> On 4/3/17, 8:57 PM, "R-help on behalf of stephen sefick" <
> r-help-bounces at r-project.org on behalf of ssefick at gmail.com>
wrote:
>
>     Hello,
>
>     I am writing an R package, and I am using system() to call a perl
> script.
>     The output of the perl script is correct except for "[A/B]"
is output
> as
>     "AB". Can someone explain this behavior. I would like to try
and fix
> this.
>     many thanks,
>
>     Stephen Sefick
>
>     --
>     Let's not spend our time and resources thinking about things that
are
> so
>     little or so large that all they really do for us is puff us up and
> make us
>     feel like gods.  We are mammals, and have not exhausted the annoying
> little
>     problems of being mammals.
>
>                                     -K. Mullis
>
>     "A big computer, a complex algorithm and a long time does not
equal
>     science."
>
>                                   -Robert Gentleman
>
>         [[alternative HTML version deleted]]
>
>     ______________________________________________
>     R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>     https://stat.ethz.ch/mailman/listinfo/r-help
>     PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
>     and provide commented, minimal, self-contained, reproducible code.
>
>
>

-- 
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods.  We are mammals, and have not exhausted the annoying little
problems of being mammals.

                                -K. Mullis

"A big computer, a complex algorithm and a long time does not equal
science."

                              -Robert Gentleman

	[[alternative HTML version deleted]]