topic PROC IML Submit / R not functioning, with no errors in log in SAS/IML Software and Matrix Computations

PROC IML Submit / R not functioning, with no errors in log

jkurka — Mon, 11 Mar 2019 19:51:23 GMT

I am trying to use Proc IML to run R code as most of the project's needed processing takes place in SAS. This piece of code runs successfully in R, but when run in SAS, nothing happens, and no errors are reported. I've successfully submitted other chunks of R code via Proc IML submit / R, so have run out of troubleshooting paths.

Any suggestions?

PROC IML ;
submit / R;
  library(lubridate)
  library(tidyverse)
  x=c(dir("X:/path/meta/ms3.out",  full.names = TRUE, ignore.case = TRUE))
  tmp1=x[1:length(x)]
    convert_csv<-function(tmp1) {
      load(tmp1) 
      fname = unlist(strsplit(tmp1,"ms3.out/"))[2]
      fname2 = unlist(strsplit(fname,".RData"))[1]
      write.csv(sib.cla.sum, file = paste("X:/path/meta/csv","/",fname2,".csv",sep=""))
    }
  lapply(tmp1,convert_csv)
endsubmit ;

Re: PROC IML Submit / R not functioning, with no errors in log

Ksharp — Tue, 12 Mar 2019 13:08:29 GMT

Try options isOK= .

PROC IML ;
submit / R isOK=OK;
.............
endsubmit ;
print OK;

Re: PROC IML Submit / R not functioning, with no errors in log

Ksharp — Tue, 12 Mar 2019 13:13:32 GMT

Better post is at IML forum @Rick_SAS is there.

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Tue, 12 Mar 2019 13:24:39 GMT

Please attatch your ms3.out file, or at least a portion of it.

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Tue, 12 Mar 2019 15:29:08 GMT

Thanks for the suggestion, but that didn't work.

isOK=OK resulted in an error

OK=isOK resulted in no change from my previous attempts.

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Tue, 12 Mar 2019 15:26:16 GMT

The files in the ms3.out folder are RData files that I'm just trying to convert to a CSV file. The communities page isn't letting me attach an RData file to this post. Any suggestions would be appreciated!

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Tue, 12 Mar 2019 15:41:35 GMT

I guess my first question is what do you mean when you say "nothing happens." Are you saying that the program runs to completion but no CSV files are created?

I suggest you verify that you have write-permission from within SAS to the directory where you are writing the CSV. I assume this directory is on the same machine that SAS is running on?

1. Simplify the program to create a simple data frame and use write.csv to write it to the directory in question.

Might as well verify that you can read the directory, too:

2. Does the program work when you just load() the data?

Presumably, one of those operations will fail.

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Tue, 12 Mar 2019 15:52:08 GMT

Yes, exactly. The program runs to completion, but no csv files are created. When I run the exact code in R, it successfully creates the csv files.

The directory is not on the hard drive of the computer, but it should be accessible. I haven't had any issues loading and creating files or new directories in the past in this directory.

It's interesting, when I split it up into 2 main chunks:

Chunk 1:

PROC IML ;
submit / R ;
  load("X:/NAYSHAW/NAYSHAW results/output_11055, 11056, 11062, 11066/meta/sleeplog.RData") #ggir log
  write.csv(sleeplog, file = paste("X:/NAYSHAW/NAYSHAW results/output_11055, 11056, 11062, 11066/meta/","/","sleeplog.csv",sep="")) #csv log
endsubmit;

and Chunk 2:

submit / R ;
  library(lubridate)
  library(tidyverse)
  x=c(dir("X:/NAYSHAW/NAYSHAW results/output_11055, 11056, 11062, 11066/meta/ms3.out",  full.names = TRUE, ignore.case = TRUE))
  tmp1=x[1:length(x)]
    convert_csv<-function(tmp1) {
      load(tmp1) 
      fname = unlist(strsplit(tmp1,"ms3.out/"))[2]
      fname2 = unlist(strsplit(fname,".RData"))[1]
      write.csv(sib.cla.sum, file = paste("X:/NAYSHAW/NAYSHAW results/output_11055, 11056, 11062, 11066/meta/csv","/",fname2,".csv",sep=""))
    }
  lapply(tmp1,convert_csv)
endsubmit ;

Chunk 1 successfully loads and writes the file. But Chunk 2 runs to completion with no resulting CSV files.

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Tue, 12 Mar 2019 16:03:22 GMT

I do not know what is going on but I think you are on the right track by breaking up the problem. Does it work if you call the lapply function with a list that contains the 'sleeplog.RData' file which works in the first chunk? How about a hard-coded list with two elements?

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Fri, 22 Mar 2019 14:50:24 GMT

I'm not following your suggestion completely as I've had a hard time picking up R. I suppose I'm confused as to why, if the code works in R, it does not work using PROC IML submit / R. It's likely I'm not understanding why the 2 are different in results. Any more suggestions would be appreciated. Or more detail on what you mean by your post.

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Sat, 23 Mar 2019 12:16:20 GMT

Depending on where SAS runs, it might not have access to (or permission for) the same directories on your PC that R is accessing.

As I've said, your best bet is to break up the problem to find out what is failing.

It might be helpful if you explain your goal. What are you trying to accomplish? It looks like you are converting R data frames to CSV files, but why? Is that so that SAS can read the CSV? If so, could you use the ImportDataSetFromR function to read the R data directly? Why go through CSV?

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Mon, 25 Mar 2019 15:27:28 GMT

Thank you Rick_SAS.

I wasn't really sure how to break up the pieces of the remaining code as it is a function.

Actually, that is exactly what I'm trying to accomplish. The file we are dealing with is created partway through an R package run. We are taking this intermediate file and doing our own processing thereafter, but doing so in SAS. So, yes we just want the RData file to be used in SAS. I will try this function.

Thanks again!

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Fri, 19 Apr 2019 23:15:27 GMT

Hi Rick,

I'm also having trouble using the ImportDataSetFromR function. The following code runs successfully, but again there is no result (no output, no listing, etc).

PROC IML ;
submit / R ;
load("X:/path/11055__049771.RData").
sib.cla.sum <- as.data.frame(sib.cla.sum)
endsubmit ;
call ImportMatrixFromR("Work.Mydata", "sib.cla.sum");
use Work.Mydata ;
show contents;
close Work.Mydata ;
QUIT ;

I followed your link but it only included the generic information. There was no accompanying syntax. Are there some tutorials on how to utilize this function and any specifications required?

Thank you!

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Sat, 20 Apr 2019 10:22:21 GMT

If you are trying to create a SAS data set, use

call ImportDATASETFromR("Work.Mydata", "sib.cla.sum");

You are calling

call ImportMATRIXFromR("Work.Mydata", "sib.cla.sum");

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Thu, 02 May 2019 22:33:36 GMT

Hi Rick,

Thank you for this correction. I made the edits and am still coming up with no results and no errors.

Here is my code:

proc options option=rlang; run ;

PROC IML ;
submit / R ;
load("X:/path/file.RData")
RData <- sib.cla.sum
endsubmit ;
	call ImportDataSetFromR("Work.Mydata", "RData");
use Work.Mydata ;
show contents;
close Work.Mydata ;

I've confirmed sib.cla.sum is a data frame within the file using attributes. This is what prints in the log:

RLANG Enables SAS to execute R language statements.
NOTE: PROCEDURE OPTIONS used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds
24
25 PROC IML ;
NOTE: IML Ready
26 submit / R ;
27 load("X:/NAYSHAW/NAYSHAW results/output_testRtoSAS/meta/ms3.out/11055__049771.RData")
28 RData <- sib.cla.sum
29 endsubmit ;
30 call ImportDataSetFromR("Work.Mydata", "RData");
31 use Work.Mydata ;
32 show contents;
33 close Work.Mydata ;

But there is no information in the output and no data set in the WORK directory. I apologize if I'm missing a simple step. Based on the SAS IML User Guide I am expecting some kind of basic output showing the data and a file saved in the work directory.

Thank you!

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Fri, 03 May 2019 11:05:52 GMT

I don't know, but the problem is probably in your data. Try the following test, which uses one of the standard R data frames:

proc options option=rlang VALUE; run ;

PROC IML ;
submit / R ;
RData <- iris        # built-in data set
is.data.frame(RData)
endsubmit ;
	call ImportDataSetFromR("Work.Mydata", "RData");
use Work.Mydata ;
show contents;
close Work.Mydata ;

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Fri, 03 May 2019 15:56:14 GMT

Thank you Rick, but running this test provided the same result. The code runs successfully, but no data set is created in the Work directory and no output is provided by SAS. I've tested this using SAS Enterprise Guide and base SAS 9.4.

I'm now thinking there is some error on how SAS is talking to R.

This is what's included in my configuration file, which is located at C:\Program Files\SASHome\SASFoundation\9.4

-RLANG
-config "C:\Program Files\SASHome\SASFoundation\9.4\nls\en\sasv9.cfg"
-SET R_HOME "C:\PROGRAM FILES\R\R-3.5.1\bin"

The R_HOME path contains the 'R.exe' file and the 'Rscript.exe' file.

The VALUE option you included results in these log statements:

Value: RLANG
Scope: SAS Session
How option value set: Config File
Config file name:
C:\Program Files\SASHome\SASFoundation\9.4\sasv9.cfg

When I run:

%put %sysget(R_HOME) ;

I get this statement in the log:

C:\PROGRAM FILES\R\R-3.5.1\bin

Thank you for your continued support and patience! I appreciate any assistance you provide.

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Fri, 03 May 2019 17:03:50 GMT

I think the R_HOME environment variable must point to the root directory of the R installation, not to the "bin" subdirectory.

Re: PROC IML Submit / R not functioning, with no errors in log

jkurka — Fri, 03 May 2019 17:30:17 GMT

Hi Rick,

I originally had the root directory 'C:\Program Files\R\R-3.5.1'. I tried referring to the subdirectory thinking that the path might need to have the actual R executable file. Neither have worked. Are you able to share some of your configurations and output using the same code so I can compare?

Thank you again!

Re: PROC IML Submit / R not functioning, with no errors in log

Rick_SAS — Fri, 03 May 2019 17:42:21 GMT

It looks like you are running Windows and that both SAS and R are installed on the same PC, right?

Please post

1. Version of SAS

2. Bitness (32-bit or 64-bit)

4. Bitness of R (it better match the bitness of SAS!)

5. How you are calling SAS (EG? Windows DMS? SAS/IML Studio? SAS Studio? University Edition?)

6. Let's make sure that R is being found. Run the following simple program and post the results:

proc iml;
submit / R;
  x <- 1:5
  x
endsubmit;
run ImportMatrixFromR(y, "x");
print y;