Needing a PIPE error workaround without allowing XCMD

schmidtt — Mon, 27 Mar 2017 21:18:54 GMT

Hello,

I am trying to run some R code from within SAS Enterprise Guide (7.13). I have a program that I am borrowing from Dr. Xin Wei, which I'll paste at the bottom of this post. Dr. Wei's JSTAT article (see: https://www.jstatsoft.org/article/view/v046c02) there has some great starter code, which I've been trying out. But they all result in PIPE errors. Here's an example:


data test;
do x=1 to 4;
array a[4] a1-a4;
do i=1 to 4;
a[i] = rannor(100);
end;
output;
end;
drop i x;
run;

%include "e:\sasroot\Proc_R\Proc_R.sas";
%Proc_R (SAS2R = test, R2SAS =);
cards4;
R> testm <- as.matrix(test)
R> eigen(testm)
;;;;
%quit;

---
ERROR: Insufficient authorization to access PIPE.
ERROR: Error in the FILENAME statement.

ERROR: No logical assign for filename PROC_R.

I have seen solutions to PIPE errors (e.g., http://support.sas.com/kb/41/058.html) by changing the server properties to allow external commands (XCMD). But that poses a security threat in my workplace. So I would rather edit portions of the Proc_R.sas file (from https://www.jstatsoft.org/article/view/v046c02) that are trying to initiate external commands. Unfortunately I don't even know how to identify these these external command attempts. Can you help me find them? And maybe even suggest alternative code? That would be so wonderful.

 ***********************************************************************************************************************
 ***********A macro that execute R scipt in base SAS********************************************************************                     
 ** MACRO Version:  1.0                                                                                               **
 ** SAS Version:    9.1.3/9.2                                                                                         **
 ** R Version:      2.14.0                                                                                            **
 ** Date:           Nov 24, 2011                                                                                      **
 ** Author:         Xin Wei, Ph.D.                                                                                    **
 ** Affiliation:    Roche Pharmaceuticals, INC                                                                        **
 ** Instruction:    This SAS macro enables native R language to be embedded in and executed along with a SAS program  **
 **                 in the Base SAS environment under Windows OS. This macro executes a user-defined R code in batch  **
 **                 mode by calling the unnamed pipe method within base SAS. The R textual and graphical output can be**
 **                 routed to the SAS output window and result viewer, respectively. Also, this macro automatically   **
 **                 converts data between SAS datasets and R data frames such that the data and results from each     **
 **                 statistical environment can be utilized by the other environment. The objective of this macro is  **
 **                 to leverage the strength of the R programming language within the SAS environment in a systematic **
 **                 manner. Moreover, this macro helps statistical programmers to learn a new statistical language    **
 **                 while staying in a familiar environment. The macro variables are described as follows:            **
 **      SAS2R      specifies the names of SAS datasets to be converted to R dataframe. Can be single file name or    **
 **                 multiple files whose names are separated by space.                                                **
 **      R2SAS      specifies the names of R dataframes to be converted to SAS datasets. Can be single file name or   **
 **                 multiple files whose names are separated by space.                                                **
 **      rpath      The full path and file names of R executable file for various R version from 2.11 to 2.14         **
 
 ***********************************************************************************************************************;


options nomerror nomprint nomlogic nosymbolgen;
options nonotes;
%macro proc_R(SAS2R=, R2SAS=);
options notes;
%GLOBAL _SAS2R _R2SAS saswork r_code;
%let _SAS2R=&SAS2R;
%let _R2SAS=&R2SAS;
%let saswork=%sysfunc(pathname(work));
data _null_;
    call symput('r_code','r_code'||trim(left(scan(put(datetime(),best.),1,'.'))));
run;
%put &r_code;
data _null_;
     file "&saswork\&r_code..r";
     infile cards4;
     input;
     put _infile_;
%mend Proc_R;

%macro quit(rpath=%str(C:\Progra~1\R\R-3.3.2\bin\R.exe));
****for R-2.11.0, use: C:\Progra~1\R\R-2.11.0\bin\R.exe*****;
****for R-2.12.0, use: C:\Progra~1\R\R-2.12.0\bin\R.exe*****;
****for R-2.13.0, use: C:\Progra~1\R\R-2.13.0\bin\R.exe*****;
****for R-2.14.0, use: C:\Progra~1\R\R-2.14.0\bin\R.exe*****;

run;
data front_code after_code body_code r_code Rlog file; delete; run;
data body_code;
     infile "&saswork\&r_code..r" length=len;
     input var1 $varying8192. len;
run;
data _null_;
	 call symput('sasdirec',"&saswork");
	 call symput('rdirec',trim(left(tranwrd("&saswork",'\','/'))));
	 call symput('rsaswork',trim(left(tranwrd("&saswork",'\','/'))));
run;	     
*****determine if customer defined code produce fixed figure*****;
%let crfg=0;
%let userdefloc=0;
data _null_;
    set body_code;
	if index(lowcase(var1),'setwd') and 
       (index(lowcase(var1),'#')=0 or index(lowcase(var1),'#')> index(lowcase(var1),'setwd')) then do;
	   call symput('userdefloc','1');
       directory=scan(var1,2,'(');
	   directory=compress(directory,'"();');
	   directory=compress(directory,"'");
   	   call symput('rdirec',trim(left(directory)));
	   directory=tranwrd(directory,'/','\');
   	   call symput('sasdirec',trim(left(directory)));
	 end;
	 if index(lowcase(var1),'.gif') or index(lowcase(var1),'.jpeg') or index(lowcase(var1),'.jpg') 
        or index(lowcase(var1),'.png') or index(lowcase(var1),'.ps') then call symput('crfg','1');
run;
*******convert sas file to csv for R import******;
%let i=1;
%do %while(%scan(&_sas2R,&i,%str( )) ne);
    %let transfer=%scan(&_sas2R,&i,%str( ));
	%let i=%eval(&i+1); 
    proc export data=&transfer outfile="&sasdirec/&transfer..csv" replace; run;
%end;

****get current time before run batch R***;
data _null_;
    call symput('nowtime',trim(left(scan(put(datetime(),best.),1,'.'))));
run;
%put $$$$&nowtime;

data front_code;
     length var1 $1000;
	 format var1 $1000.;
	 %if &userdefloc=0 %then %do;
         var1='setwd("'||"&rsaswork"||'")'; output;
	 %end;
	 var1='library(grDevices)'; output;
	 %if &crfg=0 %then %do;
	     var1='png("'||"&rdirec/_&nowtime"||'.png")'; output;
	 %end;
	 ******prepare R code use dataframe to read in SAS dataset via CSV****;
	 %let i=1;
     %do %while(%scan(&_sas2r,&i,%str( )) ne);
     %let transfer=%scan(&_sas2r,&i,%str( ));
	 %let i=%eval(&i+1); 
          var1="&transfer"||"<- read.csv('"||"&rdirec/&transfer..csv"||"')";
	      output;
	 %end;
run;

data after_code;
     length var1 $1000;
	 format var1 $1000.;
	 ******prepare R code to output csv file for sas import****;
	 %let i=1;
     %do %while(%scan(&_R2SAS,&i,%str( )) ne);
     %let transfer=%scan(&_R2SAS,&i,%str( ));
	 %let i=%eval(&i+1); 
          var1="write.csv(&transfer,'"||"&transfer..csv"||"',row.names=F)";
	      output;
	 %end;
 	 %if &crfg=0 %then %do;
	     var1='dev.off()'; output;
	 %end;
	 var1='q()'; output;
run;


*****update R code*****;
data r_code;
     set front_code body_code after_code;
run;
data _null_;
     file "&saswork/&r_code..r";
	 set r_code;
	 put var1;
run;


****get current time before run batch R***;
data _null_;
    call symput('beforetm',trim(left(put(datetime(),datetime19.))));
run;
%put $$$$&beforetm;

%let _saswork=%bquote("&rsaswork/&r_code..r");
%let _rdirec=%bquote("&rdirec/r_log_&nowtime..txt");

options noxwait xsync; 
filename proc_r pipe "&rpath CMD BATCH --vanilla --quiet
                    &_saswork  &_rdirec";
data _null_;
     infile proc_r;
run;

****get current time after run batch R***;
data _null_;
    call symput('aftertm',trim(left(put(datetime(),datetime19.))));
run;
%put $$$$&aftertm;

data rlog;
     infile "&sasdirec\r_log_&nowtime..txt" length=len;
     input var1 $varying8192. len;
run;
data rlog;
     set rlog;
	 var1=trim(left(var1));
run;
title "******************R OUTPUT***********************";
proc print data=rlog(rename=(var1=R_OUTPUT_LOG)) noobs; run;
title;

*****display R graphics*****;
%let _sasdirec=%bquote("&sasdirec");
FileName MyDir Pipe "dir &_sasdirec /a:-d";
data file;
  infile MyDir lrecl=300 truncover;
  input @1 file $100. @;
  format   file $100.;
  crtime=substr(file,1,20);
  if trim(left(scan(lowcase(file),2,'.'))) in ('gif','png','jpeg','jpg','ps') then do;
     _crtime=input(crtime,mdyampm.);
	 temp=tranwrd(file,trim(left(crtime)),'*');
	 temp=scan(temp,1,'*');
	 filename=trim(left(scan(temp,2,' ')));
  end;
run;

proc sort data=file; by descending _crtime descending filename; 
      where trim(left(scan(lowcase(file),2,'.'))) in ('gif','png','jpeg','ps'); 
run;
data _null_;
     set file;
	 if _n_=1 then do;
        call symput('fgsw',put(input("&beforetm",datetime19.)<(input(crtime,mdyampm.)+60),best.));
        temp=tranwrd(file,trim(left(crtime)),'*');
		temp2=scan(temp,1,'*');
		fgname=scan(temp2,2,' ');
		call symput('fgname',trim(left(fgname)));
	 end;
run;
%put $$$$&fgname;
%if &fgsw=1 %then %do;

ODS ESCAPECHAR='^';
ODS HTML FILE="&sasdirec\rhtml_&nowtime..html" STYLE=minimal
GPATH="&sasdirec\" GTITLE GFOOTNOTE;
ods listing close;
%global inhtml;
%let inhtml=%bquote("&sasdirec\&fgname");
DATA _NULL_;
FILE PRINT;
PUT "<IMG src=&inhtml BORDER='0'>";
RUN;
ods html close;
ods listing;
/*
goptions reset=all device=win;
goptions iback="&rdirec\&fgname" imagestyle=fit; 
proc gslide;
run;
quit; 
*/

%end;
*******convert csv file from R to SAS file******;
%let i=1;
%do %while(%scan(&_R2SAS,&i,%str( )) ne);
    %let transfer=%scan(&_R2SAS,&i,%str( ));
	%let i=%eval(&i+1); 
    proc import datafile="&sasdirec/&transfer..csv" out=&transfer replace; guessingrows=1000; run;
%end;


*options notes;
%mend;

Re: Replacing ODS HTML output for Enterprise Guide

Cynthia_sas — Wed, 22 Mar 2017 23:51:51 GMT

Hi:
I don't see where the value of &sasdirec or &inhtml are being set. I am not sure I understand how the macro you show as Proc_R.sas is being invoked. You might wish to contact the author of the macro program for more direct help.

cynthia

Re: Replacing ODS HTML output for Enterprise Guide

schmidtt — Mon, 27 Mar 2017 21:10:41 GMT

Cynthia,

Thanks so much for this post, and for your questions. They have helped point me in the right direction. I've edited my post, which might make more sense now.

Sincerely,

Teresa

topic Re: Replacing ODS HTML output for Enterprise Guide in ODS and Base Reporting

Needing a PIPE error workaround without allowing XCMD

Re: Replacing ODS HTML output for Enterprise Guide

Re: Replacing ODS HTML output for Enterprise Guide