| commit | author | age | ||
| 76bbd0 | 1 | ;ELC |
| C | 2 | ;;; Compiled |
| 3 | ;;; in Emacs version 26.1 | |
| 4 | ;;; with all optimizations. | |
| 5 | ||
| 6 | ;;; This file uses dynamic docstrings, first added in Emacs 19.29. | |
| 7 | ||
| 8 | ;;; This file does not contain utf-8 non-ASCII characters, | |
| 9 | ;;; and so can be loaded in Emacs versions earlier than 23. | |
| 10 | ||
| 11 | ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; | |
| 12 | ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; | |
| 13 | ||
| 14 | ||
| 15 | (byte-code "\300\301!\210\300\302!\207" [require cl-lib ob] 2) | |
| 16 | #@30 R-specific header arguments. | |
| 17 | (defconst org-babel-header-args:R '((width . :any) (height . :any) (bg . :any) (units . :any) (pointsize . :any) (antialias . :any) (quality . :any) (compression . :any) (res . :any) (type . :any) (family . :any) (title . :any) (fonts . :any) (version . :any) (paper . :any) (encoding . :any) (pagecentre . :any) (colormodel . :any) (useDingbats . :any) (horizontal . :any) (results (file list vector table scalar verbatim) (raw html latex org code pp drawer) (replace silent none append prepend) (output value graphics))) (#$ . 471)) | |
| 18 | #@132 Header args which are safe for R babel blocks. | |
| 19 | ||
| 20 | See `org-babel-safe-header-args' for documentation of the format of | |
| 21 | this variable. | |
| 22 | (defconst ob-R-safe-header-args (append org-babel-safe-header-args '(:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal)) (#$ . 1042)) | |
| 23 | (defvar org-babel-default-header-args:R nil) | |
| 24 | (byte-code "\300\301\302\303#\210\304\305\306\307\310DD\311\312\313\314\315\316\317& \207" [put org-babel-default-header-args:R safe-local-variable #[257 "\211<\205 \300\301\"\207" [cl-every #[257 "\211:\205 \301\"\207" [ob-R-safe-header-args org-babel-one-header-arg-safe-p] 4 "\n\n(fn PAIR)"]] 4 "\n\n(fn VALUE)"] custom-declare-variable org-babel-R-command funcall function #[0 "\300\207" [#1="R --slave --no-save"] 1 #1#] "Name of command to use for executing R code." :group org-babel :version "24.1" :type string] 10) | |
| 25 | #@13 | |
| 26 | ||
| 27 | (fn INFO) | |
| 28 | (defalias 'org-babel-edit-prep:R #[257 "\300\3018\236A\211\205 \302\303\"\205 \304\303\"\205 \305\306\"\207" [:session 2 string-prefix-p "*" string-suffix-p org-babel-R-initiate-session nil] 5 (#$ . 2015)]) | |
| 29 | #@127 R code used to transfer a table defined as a variable from org to R. | |
| 30 | ||
| 31 | This function is used when the table contains a header. | |
| 32 | (defconst ob-R-transfer-variable-table-with-header "%s <- local({\n con <- textConnection(\n %S\n )\n res <- utils::read.table(\n con,\n header = %s,\n row.names = %s,\n sep = \"\\t\",\n as.is = TRUE\n )\n close(con)\n res\n })" (#$ . 2248)) | |
| 33 | #@135 R code used to transfer a table defined as a variable from org to R. | |
| 34 | ||
| 35 | This function is used when the table does not contain a header. | |
| 36 | (defconst ob-R-transfer-variable-table-without-header "%s <- local({\n con <- textConnection(\n %S\n )\n res <- utils::read.table(\n con,\n header = %s,\n row.names = %s,\n sep = \"\\t\",\n as.is = TRUE,\n fill = TRUE,\n col.names = paste(\"V\", seq_len(%d), sep =\"\")\n )\n close(con)\n res\n })" (#$ . 2698)) | |
| 37 | #@102 Expand BODY according to PARAMS, return the expanded body. | |
| 38 | ||
| 39 | (fn BODY PARAMS &optional GRAPHICS-FILE) | |
| 40 | (defalias 'org-babel-expand-body:R #[770 "\300\301\302\303\236A\205 \303\236AC\304!C\305\236A\205$ \305\236AC$\306#\207" [mapconcat identity append :prologue org-babel-variable-assignments:R :epilogue "\n"] 11 (#$ . 3243)]) | |
| 41 | #@104 Execute a block of R code. | |
| 42 | This function is called by `org-babel-execute-src-block'. | |
| 43 | ||
| 44 | (fn BODY PARAMS) | |
| 45 | (defalias 'org-babel-execute:R #[514 "\212\300\236A\301\236A\302\303\236A\"\304\300\236\235\205 \305!\211?\205$ \306\236A?\205. \307\236A\310#C\311\312\203K \313\314\f\"C\315C#\202L \316#\262\317\n\320\232\206g \321\322\236A \"\320\232\206w \321\323\236A \"&?\205 \211\266\210)\207" [:result-params :result-type org-babel-R-initiate-session :session "graphics" org-babel-graphical-output-file :colnames :rownames org-babel-expand-body:R mapconcat identity append org-babel-R-construct-graphics-device-call "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()" "\n" org-babel-R-evaluate "yes" org-babel-pick-name :colname-names :rowname-names] 18 (#$ . 3586)]) | |
| 46 | #@93 Prepare SESSION according to the header arguments specified in PARAMS. | |
| 47 | ||
| 48 | (fn SESSION PARAMS) | |
| 49 | (defalias 'org-babel-prep-session:R #[514 "\301\"\302!\303!\204 \304\305\"\210\306 \307\310\311\312\313!\314\"\315$\216rq\210\212\316\317\307\320\321\312\313!\322\"\323\324%\"\210,\210\207" [comint-input-filter org-babel-R-initiate-session org-babel-variable-assignments:R org-babel-comint-buffer-livep error "Buffer %s does not exist or has no process" match-data make-byte-code 0 "\301\300\302\"\207" vconcat vector [set-match-data evaporate] 3 #[257 "\300\207" [nil] 2 "\n\n(fn INPUT)"] mapc 257 "\301\210\211c\210\302\303\304\"\210\305\300!\207" [1 comint-send-input nil t org-babel-comint-wait-for-output] 4 "\n\n(fn VAR)"] 12 (#$ . 4521)]) | |
| 50 | #@51 Load BODY into SESSION. | |
| 51 | ||
| 52 | (fn SESSION BODY PARAMS) | |
| 53 | (defalias 'org-babel-load-session:R #[771 "\300 \301\302\303\304\305!\306\"\307$\216\310\"r\211q\210\311\312p!!b\210\313!c\210)\211\262)\207" [current-window-configuration make-byte-code 0 "\301\300!\207" vconcat vector [set-window-configuration] 2 org-babel-prep-session:R process-mark get-buffer-process org-babel-chomp] 10 (#$ . 5279)]) | |
| 54 | #@75 Return list of R statements assigning the block's variables. | |
| 55 | ||
| 56 | (fn PARAMS) | |
| 57 | (defalias 'org-babel-variable-assignments:R #[257 "\300!\301\302\303\304\305\306!\307\"\310\311%\301\302\303\312\305\306 \"\313\"\314\315%\316\317GS\"\"\"\207" [org-babel--get-vars mapcar make-byte-code 257 "\301@A\302\300\236A\303\232\304\300\236A\303\232$\207" vconcat vector [org-babel-R-assign-elisp :colnames "yes" :rownames] 7 "\n\n(fn PAIR)" "\211\3018@\302\3018A\303\300\236A8A\304\300\236A8A#B\207" [org-babel-reassemble-table :colname-names :rowname-names] 8 "\n\n(fn I)" number-sequence 0] 12 (#$ . 5680)]) | |
| 58 | #@40 Quote field S for export to R. | |
| 59 | ||
| 60 | (fn S) | |
| 61 | (defalias 'org-babel-R-quote-tsv-field #[257 "\211;\203 \300\301\302\303\300\"\304#\300Q\207\305\306\"\207" ["\"" mapconcat identity split-string "\"\"" format "%S"] 7 (#$ . 6291)]) | |
| 62 | #@109 Construct R code assigning the elisp VALUE to a variable named NAME. | |
| 63 | ||
| 64 | (fn NAME VALUE COLNAMES-P ROWNAMES-P) | |
| 65 | (defalias 'org-babel-R-assign-elisp #[1028 "<\203n \303\304\305\306\"\"\211\203 \307\310\"\202 \311\203$ \307\312\"\202% \311@<\204/ C\262\313\314\"A@\315=\204A \203E \316\202F \317\203N \320\202O \321U\203` \322 %\202k \322 \n&\266\203\207\250\203~ \322\323\324!\325P#\207\326!\203\212 \322\323#\207;\203\260 \322\327\330\211\203\243 \331\311G\n$\210\202\253 \332\311G\330$\210\266\202#\207\322\327\333!#\207" [ob-R-transfer-variable-table-with-header ob-R-transfer-variable-table-without-header org-rm-props mapcar length cl-remove-if-not sequencep apply max 0 min orgtbl-to-tsv (:fmt org-babel-R-quote-tsv-field) hline "TRUE" "FALSE" "1" "NULL" format "%s <- %s" number-to-string "L" floatp "%s <- %S" nil remove-text-properties set-text-properties prin1-to-string] 17 (#$ . 6522)]) | |
| 66 | #@75 If there is not a current R process then create one. | |
| 67 | ||
| 68 | (fn SESSION PARAMS) | |
| 69 | (defalias 'org-babel-R-initiate-session #[514 "\303\230?\205{ \206\f \304\305\300!\205 \205 \306\236A?\307!\203& \211\202x \310 \311\312\313\314\315!\316\"\317$\216\320!\203= q\210\321\322!\210\323 \210\324 \206J \n!\325\326\"\203Y \327!\210\202K \210\330\331!\203g \332!\202r ;\203p \202r \332 !\210p)\262)\262\207" [ess-ask-for-ess-directory ess-local-process-name ess-current-process-name "none" "*R*" boundp :dir org-babel-comint-buffer-livep current-window-configuration make-byte-code 0 "\301\300!\207" vconcat vector [set-window-configuration] 2 get-buffer require ess R get-process process-get callbacks ess-wait-for-process rename-buffer bufferp buffer-name] 10 (#$ . 7471)]) | |
| 70 | #@140 Associate R code buffer with an R session. | |
| 71 | Make SESSION be the inferior ESS process associated with the | |
| 72 | current code buffer. | |
| 73 | ||
| 74 | (fn SESSION) | |
| 75 | (defalias 'org-babel-R-associate-session #[257 "\301\302!!\303 \207" [ess-local-process-name process-name get-buffer-process ess-make-buffer-current] 4 (#$ . 8256)]) | |
| 76 | #@359 An alist mapping graphics file types to R functions. | |
| 77 | ||
| 78 | Each member of this list is a list with three members: | |
| 79 | 1. the file extension of the graphics file, as an elisp :keyword | |
| 80 | 2. the R graphics device function to call to generate such a file | |
| 81 | 3. the name of the argument to this function which specifies the | |
| 82 | file to write to (typically "file" or "filename") | |
| 83 | (defvar org-babel-R-graphics-devices '((:bmp "bmp" "filename") (:jpg "jpeg" "filename") (:jpeg "jpeg" "filename") (:tikz "tikz" "file") (:tiff "tiff" "filename") (:png "png" "filename") (:svg "svg" "file") (:pdf "pdf" "file") (:ps "postscript" "file") (:postscript "postscript" "file")) (#$ . 8570)) | |
| 84 | #@66 Construct the call to the graphics device. | |
| 85 | ||
| 86 | (fn OUT-FILE PARAMS) | |
| 87 | (defalias 'org-babel-R-construct-graphics-device-call #[514 "\301\302!\303\304P!\236\206 \305\236\306\236A\307\211A@\262\3108\262\311\312\313\314\315\316 !\317\"\320\321%\322#\262\323\324 \203F \325\202G \322 \206M \322&\207" [org-babel-R-graphics-devices (:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal) file-name-extension intern ":" :png :R-dev-args nil 2 mapconcat make-byte-code 257 "\211@\300\235\203 \301\302\303@!\304\305OA#\207\306\207" vconcat vector [format ",%s=%S" symbol-name 1 nil #1=""] 6 "\n\n(fn PAIR)" #1# format "%s(%s=\"%s\"%s%s%s); tryCatch({" ","] 16 (#$ . 9234)]) | |
| 88 | (defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'") | |
| 89 | (defconst org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"") | |
| 90 | #@293 A template for an R command to evaluate a block of code and write the result to a file. | |
| 91 | ||
| 92 | Has four %s escapes to be filled in: | |
| 93 | 1. Row names, "TRUE" or "FALSE" | |
| 94 | 2. Column names, "TRUE" or "FALSE" | |
| 95 | 3. The code to be run (must be an expression, not a statement) | |
| 96 | 4. The name of the file to write to | |
| 97 | (defconst org-babel-R-write-object-command "{\n function(object,transfer.file) {\n object\n invisible(\n if (\n inherits(\n try(\n {\n tfile<-tempfile()\n write.table(object, file=tfile, sep=\"\\t\",\n na=\"nil\",row.names=%s,col.names=%s,\n quote=FALSE)\n file.rename(tfile,transfer.file)\n },\n silent=TRUE),\n \"try-error\"))\n {\n if(!file.exists(transfer.file))\n file.create(transfer.file)\n }\n )\n }\n}(object=%s,transfer.file=\"%s\")" (#$ . 10168)) | |
| 98 | #@98 Evaluate R code in BODY. | |
| 99 | ||
| 100 | (fn SESSION BODY RESULT-TYPE RESULT-PARAMS COLUMN-NAMES-P ROW-NAMES-P) | |
| 101 | (defalias 'org-babel-R-evaluate #[1542 "\203 \300&\207\301%\207" [org-babel-R-evaluate-session org-babel-R-evaluate-external-process] 13 (#$ . 11319)]) | |
| 102 | #@268 Evaluate BODY in external R process. | |
| 103 | If RESULT-TYPE equals `output' then return standard output as a | |
| 104 | string. If RESULT-TYPE equals `value' then return the value of the | |
| 105 | last statement in BODY, as elisp. | |
| 106 | ||
| 107 | (fn BODY RESULT-TYPE RESULT-PARAMS COLUMN-NAMES-P ROW-NAMES-P) | |
| 108 | (defalias 'org-babel-R-evaluate-external-process #[1285 "\302\267\202\262 \303\304!\305\306 \203 \307\202 \310\203( \203$ \311\202) \307\202) \310\306\312 \"\313\314\"%\"\210\315\316\235?\205\247 \317\235\204\201 \320\235\204\201 \321\235\204\201 \322\235\204\201 \323\235\204\201 \324\235\204\201 \325\235\204{ \326\235\204{ \327\235\204{ \330\235\203\243 \331\235\204\243 \332\333!r\211q\210\334\335\336\337\340!\341\"\342$\216\343!\210\344\345 \346\"*\262\202\247 \347\350\"\262\"\207\305\"\207\351\207" [org-babel-R-command org-babel-R-write-object-command #s(hash-table size 2 test eql rehash-size 1.5 rehash-threshold 0.8125 purecopy t data (value 6 output 172)) org-babel-temp-file "R-" org-babel-eval format "TRUE" "FALSE" "NA" "{function ()\n{\n%s\n}}()" org-babel-process-file-name noquote org-babel-R-process-value-result "none" "scalar" "verbatim" "html" "code" "pp" "file" "output" "raw" "org" "drawer" "table" generate-new-buffer " *temp*" make-byte-code 0 "\301\300!\205 \302\300!\207" vconcat vector [buffer-name kill-buffer] 2 insert-file-contents org-babel-chomp buffer-string "\n" org-babel-import-elisp-from-file (16) nil] 16 (#$ . 11595)]) | |
| 109 | #@265 Evaluate BODY in SESSION. | |
| 110 | If RESULT-TYPE equals `output' then return standard output as a | |
| 111 | string. If RESULT-TYPE equals `value' then return the value of the | |
| 112 | last statement in BODY, as elisp. | |
| 113 | ||
| 114 | (fn SESSION BODY RESULT-TYPE RESULT-PARAMS COLUMN-NAMES-P ROW-NAMES-P) | |
| 115 | (defalias 'org-babel-R-evaluate-session #[1542 "\306\267\202\221\307\310!r\211q\210\311\312\313\314\315!\316\"\317$\216\320!c\210\321\322!!\323\324\323!\210,\210\325\326!\327\330\n\203@ \331\202A \332\203S \203O \333\202T \331\202T \332\334\335 \336\"%#\210\337\340\235?\205\316 \341\235\204\250 \342\235\204\250 \343\235\204\250 \344\235\204\250 \345\235\204\250 \346\235\204\250 \347\235\204\242 \350\235\204\242 \351\235\204\242 \352\235\203\312 \353\235\204\312 \307\310!r\211q\210\311\312\313\314\315!\354\"\317$\216\355!\210\320\356 \357\"*\262\202\316 \360\361\"\262\"\207\362\320\363\364\323\365\366\365\367\370!\204\351 \371\372\"\210\373 \311\312\374\314\315!\375\"\376$\216rq\210\212\377\201C C\311\201D \201E \314\315!\201F \"\201G \201H %\fB \323\201I \322p!!b\210`d{\262|\266\362\320 D\357#c\210\201J \210@b\210\212\201K \201L A!\323\201M #\205a\201K B\323\201M #)\204p\201N \322p!!\210\202A\201I \322p!!b\210\211c\210\201O \242B\")\266\202,\262\"\"\"!\357#\207\323\207" [ess-eval-visibly-p ess-local-process-name org-babel-R-write-object-command comint-input-filter comint-output-filter-functions org-babel-R-eoe-indicator #s(hash-table size 2 test eql rehash-size 1.5 rehash-threshold 0.8125 purecopy t data (value 6 output 211)) generate-new-buffer " *temp*" make-byte-code 0 "\301\300!\205 \302\300!\207" vconcat vector [buffer-name kill-buffer] 2 org-babel-chomp process-name get-buffer-process nil ess-eval-buffer org-babel-temp-file "R-" org-babel-comint-eval-invisibly-and-wait-for-file format "TRUE" "FALSE" "NA" ".Last.value" org-babel-process-file-name noquote org-babel-R-process-value-result "none" "scalar" "verbatim" "html" "code" "pp" "file" "output" "raw" "org" "drawer" "table" [buffer-name kill-buffer] insert-file-contents buffer-string "\n" org-babel-import-elisp-from-file (16) mapconcat butlast delq mapcar #[257 "\211G\300V\205 \211\207" [0] 3 "\n\n(fn LINE)"] #[257 "\300\301\302\303\"@\"\203 \211\304\225\305O\207\207" [string-match "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)" split-string "\n" 1 nil] 6 "\n\n(fn LINE)"] org-babel-comint-buffer-livep error "Buffer %s does not exist or has no process" match-data "\301\300\302\"\207" [set-match-data evaporate] 3 #[257 "\300\207" [nil] 2 "\n\n(fn INPUT)"] comint-last-input-end org-babel-R-eoe-output comint-prompt-regexp "" 257 "\300\211\242P\240\207" [] 4 "\n\n(fn TEXT)" process-mark inferior-ess-send-input re-search-forward regexp-quote t accept-process-output split-string] 23 (#$ . 13065)]) | |
| 116 | #@128 R-specific processing of return value. | |
| 117 | Insert hline if column names in output have been requested. | |
| 118 | ||
| 119 | (fn RESULT COLUMN-NAMES-P) | |
| 120 | (defalias 'org-babel-R-process-value-result #[514 "\211\203\f @\300ABB\207\207" [hline] 5 (#$ . 15883)]) | |
| 121 | (provide 'ob-R) | |
