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was passing all test, but either found or created a new bug in R code evaluation
This commit is contained in:
Eric Schulte
parent
73163718ca
commit
cc622b1383
173
rorg.org
173
rorg.org
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@ -18,38 +18,6 @@
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argument, and the default behavior could be controlled through a
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configuration variable.
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** TODO results name
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In order to do this we will need to start naming our results.
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Since the source blocks are named with =#+srcname:= lines we can
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name results with =#+resname:= lines (if the source block has no
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name then no name is given to the =#+resname:= line on creation,
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otherwise the name of the source block is used).
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This will have the additional benefit of allowing results and
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source blocks to be located in different places in a buffer (and
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eventually in different buffers entirely).
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#+srcname: developing-resnames
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#+begin_src emacs-lisp :results silent
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'schulte
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#+end_src
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Once source blocks are able to find their own =#+resname:= lines
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we then need to...
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#+srcname: sbe-w-new-results
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#+begin_src emacs-lisp :results replace
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(sbe "developing-resnames")
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#+end_src
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#+resname:
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: schulte
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*** TODO change the results insertion functions to use these lines
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*** TODO teach references to resolve =#+resname= lines.
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** TODO re-implement R evaluation using ess-command or ess-execute
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I don't have any complaints with the current R evaluation code or
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behaviour, but I think it would be good to use the ESS functions
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@ -245,6 +213,37 @@ mean(mean(vec))
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posterity. Same for a shell session either in a *shell* buffer, or
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pasted from another terminal emulator. And python of course.
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** DONE results name
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In order to do this we will need to start naming our results.
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Since the source blocks are named with =#+srcname:= lines we can
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name results with =#+resname:= lines (if the source block has no
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name then no name is given to the =#+resname:= line on creation,
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otherwise the name of the source block is used).
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This will have the additional benefit of allowing results and
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source blocks to be located in different places in a buffer (and
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eventually in different buffers entirely).
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#+srcname: developing-resnames
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#+begin_src emacs-lisp :results silent
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'schulte
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#+end_src
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Once source blocks are able to find their own =#+resname:= lines
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we then need to...
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#+srcname: sbe-w-new-results
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#+begin_src emacs-lisp :results replace
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(sbe "developing-resnames")
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#+end_src
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#+resname:
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: schulte
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*** TODO change the results insertion functions to use these lines
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*** TODO teach references to resolve =#+resname= lines.
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** DONE litorgy tests litorgy [1/1]
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since we are accumulating this nice collection of source-code blocks
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in the sandbox section we should make use of them as unit tests.
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@ -424,13 +423,40 @@ example in the [[* emacs lisp source reference][emacs lisp source reference]].
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* Bugs [6/8]
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* Bugs [7/9]
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** TODO R code execution seems to choke on certain inputs
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#+srcname: set-debug-on-error
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#+begin_src emacs-lisp :results silent
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(setq debug-on-error t)
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#+end_src
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#+srcname: bug-numerical-table
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#+begin_src emacs-lisp :results silent
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'(1 2 3)
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#+end_src
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#+srcname: bug-R-number-evaluation
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#+begin_src R :var table=bug-numerical-table :results silent
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mean(table)
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#+end_src
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** TODO cursor movement when evaluating source blocks
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E.g. the pie chart example. Despite the save-window-excursion in
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litorgy-execute:R. (I never learned how to do this properly: org-R
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jumps all over the place...)
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** TODO with :results replace, non-table output doesn't replace table output
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** DEFERRED org bug/request: prevent certain org behaviour within code blocks
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E.g. [[]] gets recognised as a link (when there's text inside the
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brackets). This is bad for R code at least, and more generally
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could be argued to be inappropriate. Is it difficult to get org to
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ignore text in code blocks? [DED]
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I believe Carsten addressed this recently on the mailing list with
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the comment that it was indeed a difficult issue. I believe this
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may be one area where we could wait for an upstream (org-mode) fix.
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** DONE with :results replace, non-table output doesn't replace table output
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And vice versa. E.g. Try this first with table and then with len(table) [DED]
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#+begin_src python :var table=sandbox :results replace
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table
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@ -461,16 +487,6 @@ This would have a couple of benefits...
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Thoughts? If no-one objects, I believe I will implement the labeling
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of results.
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** DEFERRED org bug/request: prevent certain org behaviour within code blocks
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E.g. [[]] gets recognised as a link (when there's text inside the
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brackets). This is bad for R code at least, and more generally
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could be argued to be inappropriate. Is it difficult to get org to
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ignore text in code blocks? [DED]
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I believe Carsten addressed this recently on the mailing list with
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the comment that it was indeed a difficult issue. I believe this
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may be one area where we could wait for an upstream (org-mode) fix.
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** DONE extra quotes for nested string
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Well R appears to be reading the tables without issue...
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@ -575,40 +591,41 @@ Evaluate all the cells in this table for a comprehensive test of the
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litorgy functionality.
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#+TBLNAME: litorgy-tests
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| functionality | block | arg | expected | results | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| basic evaluation | | | | | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| emacs lisp | basic-elisp | | 5 | 5 | pass |
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| shell | basic-shell | | 6 | 6 | pass |
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| ruby | basic-ruby | | litorgy | litorgy | pass |
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| python | basic-python | | hello world | hello world | pass |
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| R | basic-R | | 13 | 13 | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| tables | | | | | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| emacs lisp | table-elisp | | 3 | 3 | pass |
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| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass |
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| python | table-python | | 5 | 5 | pass |
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| R | table-R | | 3.5 | 3.5 | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| source block references | | | | | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| all languages | chained-ref-last | | Array | Array | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| source block functions | | | | | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| emacs lisp | defun-fibb | | fibbd | fibbd | pass |
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| run over | Fibonacci | 0 | 1 | 1 | pass |
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| a | Fibonacci | 1 | 1 | 1 | pass |
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| variety | Fibonacci | 2 | 2 | 2 | pass |
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| of | Fibonacci | 3 | 3 | 3 | pass |
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| different | Fibonacci | 4 | 5 | 5 | pass |
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| arguments | Fibonacci | 5 | 8 | 8 | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| bug fixing | | | | | pass |
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|-------------------------+------------------+-----+-------------+-------------+------|
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| simple ruby arrays | ruby-array-test | | 3 | 3 | pass |
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| functionality | block | arg | expected | results | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| basic evaluation | | | | | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| emacs lisp | basic-elisp | | 5 | 5 | pass |
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| shell | basic-shell | | 6 | 6 | pass |
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| ruby | basic-ruby | | litorgy | litorgy | pass |
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| python | basic-python | | hello world | hello world | pass |
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| R | basic-R | | 13 | 13 | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| tables | | | | | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| emacs lisp | table-elisp | | 3 | 3 | pass |
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| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass |
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| python | table-python | | 5 | 5 | pass |
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| R | table-R | | 3.5 | 3.5 | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| source block references | | | | | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| all languages | chained-ref-last | | Array | Array | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| source block functions | | | | | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| emacs lisp | defun-fibb | | fibbd | fibbd | pass |
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| run over | Fibonacci | 0 | 1 | 1 | pass |
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| a | Fibonacci | 1 | 1 | 1 | pass |
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| variety | Fibonacci | 2 | 2 | 2 | pass |
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| of | Fibonacci | 3 | 3 | 3 | pass |
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| different | Fibonacci | 4 | 5 | 5 | pass |
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| arguments | Fibonacci | 5 | 8 | 8 | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| bug fixing | | | | | pass |
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|-------------------------+-------------------------+-----+-------------+-------------+-------------------------------|
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| simple ruby arrays | ruby-array-test | | 3 | 3 | pass |
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| R number evaluation | bug-R-number-evaluation | | 2 | #ERROR | expected "2" but was "#ERROR" |
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#+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
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** basic tests
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