From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code? Date: Fri, 07 Feb 2014 20:22:20 +0100 Message-ID: <52F5326C.7010505@krugs.de> References: <52F498AE.6090802@krugs.de> <87siruamo3.fsf@gmail.com> Reply-To: Rainer@krugs.de Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="MTva44TcTDgpaNWepNQRQcGbcNoskeONV" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35449) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WBr0U-0006uo-8n for emacs-orgmode@gnu.org; Fri, 07 Feb 2014 14:22:43 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1WBr0O-0006Ln-Cd for emacs-orgmode@gnu.org; Fri, 07 Feb 2014 14:22:34 -0500 Received: from mail-wg0-f41.google.com ([74.125.82.41]:36819) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1WBr0O-0006Ka-4L for emacs-orgmode@gnu.org; Fri, 07 Feb 2014 14:22:28 -0500 Received: by mail-wg0-f41.google.com with SMTP id n12so1027438wgh.2 for ; Fri, 07 Feb 2014 11:22:27 -0800 (PST) In-Reply-To: <87siruamo3.fsf@gmail.com> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric Schulte Cc: emacs-orgmode This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --MTva44TcTDgpaNWepNQRQcGbcNoskeONV Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable On 02/07/14, 17:47 , Eric Schulte wrote: > Rainer M Krug writes: >=20 >> On 02/07/14, 07:18 , John Hendy wrote: >>> Greetings, >>> >>> >>> I don't usually tangle, but am creating a code file to go along with = a >>> presentation I'm giving this weekend so that attendees can try things= >>> out afterward by cloning my github repo where all the data and >>> necessary files are stored. >>> >>> In my presentation (Beamer), I create plots via the R pdf() device, >>> and noticed that all of the tangled code where plots are generated >>> contains the following: >>> >>> pdf(file=3D"file.pdf"); tryCatch({ >>> >>> code block contents here >>> >>> },error=3Dfunction(e){plot(x=3D-1:1, y=3D-1:1, type=3D'n', xlab=3D'',= ylab=3D'', >>> axes=3DFALSE); text(x=3D0, y=3D0, labels=3De$message, col=3D'red'); >>> paste('ERROR', e$message, sep=3D' : ')}); dev.off() >>> >>> Is there a way to omit this? >> >> This is a bug which must have been introduced some time ago - in the >> stock version of emacs (Org-mode version 7.9.3f >> (release_7.9.3f-17-g7524ef @ >> /usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not >> tangle the enclosing commands to create graphics, but in 8.2 it does (= I >> don't have an older version at hand to go further back). >> >=20 > I believe this was introduced by your commit eaa3a761d. Reversion of > which with the following should provide a temporary workaround. I checked it with version 8.2, which was, as far as I remember, before my change of the R code to include the error handling, and the pdf(...) =2E.. dev.off() was in the tangled file as well - so the behaviour must have been introduced earlier. The only change I did was to change the R code, so no change in the behavior if it is tangled or not. I will look at it again on Monday to go back through the released versions to narrow down where this had changed. >=20 > git revert eaa3a761d I don't think that this actually changes much - only that the enclosing code will become pdf(...) THE CODE dev.off() Cheers, Rainer >=20 > Perhaps the try/catch code should be moved from org-babel-expand-body:R= > to org-babel-execute:R. Alternately, the code should stay as is and yo= u > should use the no-expand header argument during tangling. >=20 > I'm not sure which makes the most sense, but I'd lean towards the > former. >=20 > Best, >=20 >> >>> >>> I'm guessing this is here to create a blank plot with the error as th= e >>> output when something goes awry? >> >> Yes. >> >>> >>> I checked around variable completions of org-babel-tangle-* and >>> searched google for terms like "org babel tangle try catch" but am no= t >>> finding anything that looks like what I need. >> >> There is nothing, as it should not be tangled. The enclosing commands >> concern the export, but not tangling, >> >> I agree that the :result graphics header argument caused commands shou= ld >> not be in the tangled file. >> >> Another question is about the :epilogue and :prologue which I think >> should be present (haven't checked if they are...). >> >> Cheers, >> >> Rainer >> >> >>> >>> >>> Thanks, >>> John >>> >=20 --=20 Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer@krugs.de Skype: RMkrug --MTva44TcTDgpaNWepNQRQcGbcNoskeONV Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJS9TJwAAoJENvXNx4PUvmChfwH/jJLc2TpDjMaOub7gnKNSAJT n7zGr4YAnGaVeGMtgLdg1eYA43ci1pxLDucWT51Z7hnQyUcOffgZEJB9l++dUAHO DQkmBFpza3tiEFbYhjWMW0XP34cZSYeS/BmdwzMS+TqEN1B8HRhACl7bS4BArmqW SlHD5JwTwjF7e0lCPRsUYu83be/5IKdviLWbB7CSWGYIxB0jtub2Li12Q+LRJBeZ perAZzW3/DtD4P8OCs8hQ1Sjz92kw+XssVk9Oc8hCWgQhtqNyPrT1SUE0tLYQS6R kJ+0bdL+m/IEtZPTHbcBiv1MOfSdS+vroTwoREQOCzx9tSnM1PmlHPkXH+2mAkY= =uiVu -----END PGP SIGNATURE----- --MTva44TcTDgpaNWepNQRQcGbcNoskeONV--