gmp26/README.md

## README.md

      
    Raw
  

              README.md
            
          
    I now have one failing case and three passing cases...
For the failing case, start test.clj in a Calva Babashka REPL. This is how I was testing...
clj꞉test꞉> 
; Evaluating file: test.clj
{:exit 1, :out "", :err "Error in print(tx_sex_m) : object 'tx_sex_m' not found\nExecution halted\n"}

This is the issue I was reporting
Without bb this is what to expect:
$ Rscript adjcox.R
[1] 0

Here are the passing cases:
From the bb terminal repl
$ bb
...
user=> (babashka.process/sh ["ls"])
{:proc #object[java.lang.ProcessImpl 0x25c0c982 "Process[pid=21366, exitValue=0]"], :exit 0, :in #object[java.lang.ProcessImpl$ProcessPipeOutputStream 0xb048e81 "java.lang.ProcessImpl$ProcessPipeOutputStream@b048e81"], :out "adjcox.R\nadjcox.Rout\nfoo.txt\nparams.csv\n", :err "", :prev nil, :cmd ["ls"]}
user=> (babashka.process/sh ["Rscript" "adjcox.R"])
{:proc #object[java.lang.ProcessImpl 0x9d1d8c3 "Process[pid=21750, exitValue=0]"], :exit 0, :in #object[java.lang.ProcessImpl$ProcessPipeOutputStream 0x185eca3d "java.lang.ProcessImpl$ProcessPipeOutputStream@185eca3d"], :out "[1] 0\n", :err "", :prev nil, :cmd ["Rscript" "adjcox.R"]}

as expected
Also surprisingly
bb test.clj
{:exit 0, :out "[1] 0\n", :err ""}

as expected.
Also (even more surprisingly) from the babashka terminal repl:
user=> (babashka.process/sh ["Rscript" "adjcox.R"])
{:proc #object[java.lang.ProcessImpl 0x9d1d8c3 "Process[pid=21750, exitValue=0]"], :exit 0, :in #object[java.lang.ProcessImpl$ProcessPipeOutputStream 0x185eca3d "java.lang.ProcessImpl$ProcessPipeOutputStream@185eca3d"], :out "[1] 0\n", :err "", :prev nil, :cmd ["Rscript" "adjcox.R"]}

as expected.
So we are only seeing the issue in the Calva REPL.

  
## adjcox.R
# Run from the R source directory
# params.csv should be in the same directory
param <- read.csv("params.csv") # In RStudio, param will appear in the environment
attach(param)
print(tx_sex_m) # should return "[1] 0"


## params.csv

          
            tx_sex_m
            tx_sex_f
            tx_age_2
            tx_age_3
            tx_age_4
            tx_age_5
            tx_age_6
            tx_age_7
            tx_eth_wh
            tx_eth_nonwh
            tx_bld_o
            tx_bld_a
            tx_bld_b
            tx_bld_ab
            tx_match_1
            tx_match_2
            tx_match_3
            tx_graft_0
            tx_graft_1
            tx_dialysis_1
            tx_dialysis_2
            tx_sens_1
            tx_sens_2
            tx_diabetes_1
            tx_diabetes_2
            rem_sex_m
            rem_sex_f
            rem_age_2
            rem_age_3
            rem_age_4
            rem_age_5
            rem_age_6
            rem_age_7
            rem_eth_wh
            rem_eth_nonwh
            rem_bld_o
            rem_bld_a
            rem_bld_b
            rem_bld_ab
            rem_match_1
            rem_match_2
            rem_match_3
            rem_graft_0
            rem_graft_1
            rem_dialysis_1
            rem_dialysis_2
            rem_sens_1
            rem_sens_2
            rem_diabetes_1
            rem_diabetes_2
            dth_sex_m
            dth_sex_f
            dth_age_2
            dth_age_3
            dth_age_4
            dth_age_5
            dth_age_6
            dth_age_7
            dth_eth_wh
            dth_eth_nonwh
            dth_bld_o
            dth_bld_a
            dth_bld_b
            dth_bld_ab
            dth_match_1
            dth_match_2
            dth_match_3
            dth_graft_0
            dth_graft_1
            dth_dialysis_1
            dth_dialysis_2
            dth_sens_1
            dth_sens_2
            dth_diabetes_1
            dth_diabetes_2

            
              0
              -0.08932
              0.55643
              0.41619
              0.1883
              0
              -0.23215
              -0.429
              0
              -0.05609
              0
              0.63663
              -0.02221
              0.63663
              0
              -0.32047
              -0.68447
              0
              -0.42997
              0
              0.23561
              0
              -0.79469
              0
              -0.13378
              0
              -0.15065
              -0.93236
              -0.58193
              -0.36876
              0
              0.55684
              1.4442
              0
              -0.17259
              0
              0.26513
              0.03992
              0.26513
              0
              -0.16539
              -0.39542
              0
              -0.17259
              0
              -0.22529
              0
              0.10413
              0
              0.23813
              0
              -0.13832
              -1.49163
              -0.86431
              -0.43495
              0
              0.18012
              0.25913
              0
              -0.26034
              0
              0.26473
              0.08114
              0.26473
              0
              0.07006
              -0.07087
              0
              0.26165
              0
              -0.33903
              0
              0.09477
              0
              0.73486

## test.clj
(ns test
  (:require [clojure.java.shell :refer [sh]]))

(sh "ls")
;; => {:exit 0, :out "adjcox.R\nadjcox.Rout\nfoo.txt\nparams.csv\ntest.clj\n", :err ""}

(sh "Rscript" "adjcox.R")
;; => {:exit 1, :out "", :err "Error in print(tx_sex_m) : object 'tx_sex_m' not found\nExecution halted\n"}
	# Run from the R source directory
	# params.csv should be in the same directory
	param <- read.csv("params.csv") # In RStudio, param will appear in the environment
	attach(param)
	print(tx_sex_m) # should return "[1] 0"
	tx_sex_m	tx_sex_f	tx_age_2	tx_age_3	tx_age_4	tx_age_5	tx_age_6	tx_age_7	tx_eth_wh	tx_eth_nonwh	tx_bld_o	tx_bld_a	tx_bld_b	tx_bld_ab	tx_match_1	tx_match_2	tx_match_3	tx_graft_0	tx_graft_1	tx_dialysis_1	tx_dialysis_2	tx_sens_1	tx_sens_2	tx_diabetes_1	tx_diabetes_2	rem_sex_m	rem_sex_f	rem_age_2	rem_age_3	rem_age_4	rem_age_5	rem_age_6	rem_age_7	rem_eth_wh	rem_eth_nonwh	rem_bld_o	rem_bld_a	rem_bld_b	rem_bld_ab	rem_match_1	rem_match_2	rem_match_3	rem_graft_0	rem_graft_1	rem_dialysis_1	rem_dialysis_2	rem_sens_1	rem_sens_2	rem_diabetes_1	rem_diabetes_2	dth_sex_m	dth_sex_f	dth_age_2	dth_age_3	dth_age_4	dth_age_5	dth_age_6	dth_age_7	dth_eth_wh	dth_eth_nonwh	dth_bld_o	dth_bld_a	dth_bld_b	dth_bld_ab	dth_match_1	dth_match_2	dth_match_3	dth_graft_0	dth_graft_1	dth_dialysis_1	dth_dialysis_2	dth_sens_1	dth_sens_2	dth_diabetes_1	dth_diabetes_2
	0	-0.08932	0.55643	0.41619	0.1883	0	-0.23215	-0.429	0	-0.05609	0	0.63663	-0.02221	0.63663	0	-0.32047	-0.68447	0	-0.42997	0	0.23561	0	-0.79469	0	-0.13378	0	-0.15065	-0.93236	-0.58193	-0.36876	0	0.55684	1.4442	0	-0.17259	0	0.26513	0.03992	0.26513	0	-0.16539	-0.39542	0	-0.17259	0	-0.22529	0	0.10413	0	0.23813	0	-0.13832	-1.49163	-0.86431	-0.43495	0	0.18012	0.25913	0	-0.26034	0	0.26473	0.08114	0.26473	0	0.07006	-0.07087	0	0.26165	0	-0.33903	0	0.09477	0	0.73486
	(ns test
	(:require [clojure.java.shell :refer [sh]]))

	(sh "ls")
	;; => {:exit 0, :out "adjcox.R\nadjcox.Rout\nfoo.txt\nparams.csv\ntest.clj\n", :err ""}

	(sh "Rscript" "adjcox.R")
	;; => {:exit 1, :out "", :err "Error in print(tx_sex_m) : object 'tx_sex_m' not found\nExecution halted\n"}