(ob-session-async-R-simple-session-async-output):
(ob-session-async-R-named-output):
(ob-session-async-R-output-drawer): Force no truncation of output
lines in ESS. Otherwise, the expected output may be split into
multiple lines.
Note that we do not want to override the output splitting outside
tests - this is what users may prefer for :results output. And
:results value is not affected.
Link: https://orgmode.org/list/87ilduqrem.fsf@localhost
* ob-R.el (org-babel-R-assign-elisp): Use the patch from
ccberry@health.ucsd.edu, to print org-list as a one column table as it
was the case in release_9.5. The break in R is due commit b4e437f96 *
ob-core: Resolve named list references to simple lists.
* test-ob-R.el (ob-R-nested-list): New function to test that org list
with multiple level are handled as expected in R.
see https://list.orgmode.org/87bkofh0ir.fsf@localhost/ for context.
* test-ob-R.el (ob-session-R-result-output): This test will check if
output is printed to buffer in a session with :results output. This
test is to prevent the bug mentioned in https://list.orgmode.org/877czca7oj.fsf@u-bordeaux.fr/
does not happen again.
Mainly, add the corresponding cookie, but also add various `require`s
so that the compiler knows which vars should be trated as dynbound.
This does not fix all the warnings, but does try to eliminate
all those about "unused" variables. For the variables truly unused,
the patch usually adds an underscore to their name to silence the warning.
Some of the fixes affect files which already used `lexical-binding`.
Not sure why the test worked before: maybe because the tests were run
without compiling them first (which could cause some of the
missing `require`d packages to be autoloaded before we got to the
problematic code, thus hiding the problem)?
I found some suspicious code, for which I added FIXMEs.
There are also a few changes to the main files.
* lisp/org-protocol.el (org-protocol-check-filename-for-protocol):
Don't call `server-edit` if it's not yet defined. [ Needed to get
the tests to pass. ]
* lisp/ob-core.el (org-babel-temporary-directory)
(org-babel-temporary-stable-directory): Always define (and use nil
if we don't want to create a directory for it). Simplify the code based
on the fact that (defvar V E) only evaluates E if V is not yet `boundp`.
(org-babel-temp-file, org-babel-temp-stable-file)
(org-babel-remove-temporary-directory)
(org-babel-remove-temporary-stable-directory): Adjust accordingly.
* lisp/org.el (org-log-beginning): Add FIXME.
* testing/org-test.el: Require `org` and `org-id`.
(org-id-locations-file): Don't `defconst` it.
(org-test-at-id, org-test-in-example-file, org-test-at-marker)
(org-test-with-temp-text, org-test-with-temp-text-in-file): Move edebug
specs into `declare` (and simplify them).
(org-test-with-tramp-remote-dir--worker): Declare dynbound tramp vars.
(org--compile-when): Fix quoting of `exp`.
(org-test-load): Tweak regexps.
* testing/org-batch-test-init.el: Tweak regexp, remove dead code and
add a FIXME about it.
* testing/lisp/test-ox.el: Require `ox` instead of
erroring out if it's not already loaded. Also require `org-inlinetask`.
(org-test-with-parsed-data): Silence warnings when `info` is not used.
(test-org-export/bind-keyword): Add FIXME.
* testing/lisp/test-ox-publish.el: Require `org-test` and `ox-publish`.
(test-org-publish/resolve-external-link): Expose lambdas to
the compiler. Remove unused var `ids`.
(test-org-publish/get-project-from-filename): Remove unused var `file`.
* testing/lisp/test-org.el: Require `org-macs`, `org`,
`org-inlinetask`, `org-refile`, and `org-agenda`.
(test-org/org-read-date): Declare `org-time-was-given` as dynbound.
(test-org/set-regexps-and-options): Add FIXME.
* testing/lisp/test-org-timer.el: Require `org-timer`.
* testing/lisp/test-org-table.el: Require `ox`.
* testing/lisp/test-org-protocol.el: Require `org-protocol` instead of
erroring out if it's not already loaded. Also require `capture`, and
add missing `provide` statement.
* testing/lisp/test-org-pcomplete.el: Require `org`.
* testing/lisp/test-org-list.el: Require `org-list` and `org`.
* testing/lisp/test-org-lint.el: Require `org-footnote` and `org-lint`.
* testing/lisp/test-org-footnote.el: Require `org-footnote`.
* testing/lisp/test-org-element.el: Require `org-element` instead of
erroring out if it's not already loaded. Also require `org` and
`org-inlinetask`.
* testing/lisp/test-org-duration.el: Require `org-duration`.
* testing/lisp/test-org-datetree.el: Require `org-datetree`.
* testing/lisp/test-org-colview.el: Require `org-colview`,
`org-duration`, and `org-inlinetask`.
* testing/lisp/test-org-clock.el: Require `org-duration` and `org-clock`.
* testing/lisp/test-org-archive.el: Require `org-archive`.
* testing/lisp/test-org-agenda.el
(test-org-agenda/bulk-custom-arg-func): Add FIXME.
* testing/lisp/test-ol.el: Require `ol` and `org-id`.
(test-org-link/store-link): Declare `org-store-link-props` and add FIXME.
* testing/lisp/test-oc.el (test-org-cite/export-capability): Add FIXME.
* testing/lisp/test-ob.el: Require `ob-core`, `org-src`, `ob-ref`,
and `org-table`.
(test-ob/eval-header-argument): Rename `foo` to `test-ob--foo` and
declare it as dynbound.
(test-ob/blocks-with-spaces, test-ob/specific-colnames): Add FIXME.
(test-ob/noweb-expansions-in-cache):
Declare `noweb-expansions-in-cache-var` as dynbound.
* testing/lisp/test-ob-tangle.el: Require `org` and `ob-tangle`.
* testing/lisp/test-ob-shell.el:
* testing/lisp/test-ob-python.el: Require `ob-core`.
* testing/lisp/test-ob-lob.el: Require `ob-lob`.
(temporary-value-for-test): Declare as dynbound.
* testing/lisp/test-ob-plantuml.el: Require `ob-plantuml` instead of
erroring out if it's not already loaded.
* testing/lisp/test-ob-lilypond.el: Require `ob-lilypond` instead of
erroring out if it's not already loaded. Use `with-current-buffer`.
* testing/lisp/test-ob-julia.el: Require `ob-core`.
* testing/lisp/test-ob-java.el (org-babel-temporary-directory):
Remove dead code now that `org-babel-temporary-directory` is always bound.
* testing/lisp/test-ob-exp.el: Require `ob-exp`, `org-src`, and `org-test`.
(ob-exp/evaluate-all-executables-in-order):
Declare `*evaluation-collector*` as dynbound.
* testing/lisp/test-ob-emacs-lisp.el (ob-emacs-lisp/dynamic-lexical-edit)
(ob-emacs-lisp/dynamic-lexical-execute):
Rename dynbound var to `ob-emacs--x` and declare it as such.
* testing/lisp/test-ob-R.el: Require `ob-core`.
(ess-ask-for-ess-directory, ess-history-file): Declare vars.
* lisp/ob-R.el (ob-session-async-R-indicator): Add constant
representing a prefix R to identity session.
(ob-session-async-org-babel-R-evaluate-session): New function to
evaluate R src block asynchrously.
(ob-session-async-R-value-callback): New function that calls back
the result of the asynchronous evaluation.
(org-babel-R-evaluate): Add `async' parameter and call
`ob-session-async-org-babel-R-evaluate-session' if `async'
parameter is present.
(org-babel-execute:R): Call `org-babel-comint-use-async' to check
if async is among `params' and add async parameter to
`org-babel-R-evaluate'.
* testing/lisp/test-ob-R.el: Add 7 more tests for async
evaluations, also taken from the `ob-session-async' package.
This is almost a carbon copy of Jack Kamm's `ob-session-async'.
The original source code can be found
https://github.com/jackkamm/ob-session-async.
Please refer to the following thread to trace back the discussion
on async evaluation in R:
https://list.orgmode.org/87eed9g9p6.fsf@gmail.com/
* testing/lisp/test-ob-R.el (ert-deftest test-ob-r/NA-blank): new test
for :results value. Make sure that NA values in R data.frames are
empty string instead of nil previously
see https://orgmode.org/list/87pn1dufm2.fsf@gmail.com/
* testing/lisp/test-ob-R.el (test-ob-r/output-with-<>): new test for output
angle brackets
(test-ob-R/output-nonprinted): New test for output results that aren't
explicitly printed. (Here all the lines are expected to be printed
not just the last one)
Patch suggested by Jack Kamm:
https://orgmode.org/list/87h7slgbi5.fsf@gmail.com/
* test-ob-R.el: (test-ob-R/simple-session, test-ob-R/results-file)
tests start sessions. As a consequence `ess-ask-for-ess-directory'
and `ess-history-file' are let bound to `nil' to avoid prompting for
the startup directory and using a history file.
Bug Reported by: Achim Gratz
Subject: [Bug] Testing: ESS (*R*, R (newest)) starting data directory?
Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/104424>
* lisp/ob-R.el: org-babel-R-evaluate-external-process and
org-babel-R-evaluate-session trim the extraneous newlines from the
end of R output.
* testing/lisp/test-ob-R.el: test-ob-R/results-file tests that
`:results file' yields one line enclosed in square brackets for a
result like "abc/def.ghi".
Fixes issue noted by Andreas Leha
Subject: [babel] return file from R
Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/103658>
* lisp/ob-R.el (org-babel-R-initiate-session): Protect against use of
unbound variable `ess-ask-for-ess-directory´. The default for this
variable is true, so act accordingly if it is found unbound.
* lisp/ob-R.el: Remove initialization with `nil´ from
`ess-ask-for-ess-directory´ and `ess-local-process-name´. Remove
second declaration for `ess-local-process-name´.
* testing/lisp/test-ob-R.el (test-ob-R/simple-session): Bind
`ess-ask-for-ess-directory´ to nil to facilitate batch testing.
I started from the 78ec8e commit then cherry-picked and squashed
commits that have been done in master since then, except the bad
commits that overwrote the tree (in master) with the tree in maint.
This commit also bumps the version number to 7.8.06.
The only "fix" that was made between 78ec8e and the previous commit
is e0072f which has been reported to break stuff.
This fixes a wrong merge that should not have happened:
commit 7e903a merges the master branch into the maint branch,
while we really want to keep the maint branch a bugfix-only
branch.
This commit reverts back the maint branch to its state before
merging the master branch. From there, we will fix remaining
problems with the maint branch (e.g. copyright issues) then
release this maint branch as Org-mode 7.8.05.
* testing/lisp/test-ob-R.el (featurep): Signal missing dependencies
with an error rather than a throw.
* testing/org-test.el (missing-test-dependency): Define the error
signal for missing dependencies.
(org-test-for-executable): Signal missing dependencies with an error
rather than a throw.
(org-test-load): Define an expected failing test for each file with
missing dependencies.
* testing/org-test.el (org-exe-not-found): An error type used to
signal a missing executable
(org-test-for-executable): A function used by test files to throw an
error if a required executable is not present.
(org-test-load): Simply skip files for which the required
executables are not present.
* testing/lisp/test-ob-R.el: Conditional loading.
* testing/lisp/test-ob-awk.el: Conditional loading.
* testing/lisp/test-ob-fortran.el: Conditional loading.
Gerard Vermeulen
Ihor Radchenko
Jeremie Juste
Stefan Monnier
Jeremie Juste
Stefan Kangas
Bastien
Charles Berry
Bastien Guerry
Achim Gratz
Eric Schulte
Eric Schulte