[Rd] One possible cause for incorrect symbols in X11() output
There have been spasmodic reports of symbols such as pi and infinity in plotmath being reproduced incorrectly on the X11 device on some Linux systems (at least Ubuntu 10 and Fedora 12/13), and we've managed to track down one cause whilst investigating PR#14355. Some systems have Wine and hence the Wine symbol font installed. 'fontconfig', which is used by cairographics in X11(type='cairo') and many other applications, prefers the Wine symbol font to the standard Type 1 URW font, and seems to misinterpret its encoding. You may well have Wine installed without realizing it (as I did) -- it is increasingly common as a dependency of other software. The best test is to run % fc-match symbol s05l.pfb: Standard Symbols L Regular This is the result on a system without Wine: if you see % fc-match symbol symbol.ttf: Symbol Regular you at least potentially have the problem. A good test is to look at ?points and run the function TestChars() defined there as TestChars(font=5) If you do have the problem, a workaround is to add the following lines to ~/.fonts.conf or /etc/fonts/local.conf (which you may need to create): match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match and repeat the fc-match test to check that it worked. (This workaround was culled from https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/551977 ) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On 19/08/10 09:55 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: There have been spasmodic reports of symbols such as pi and infinity in plotmath being reproduced incorrectly on the X11 device on some Linux systems (at least Ubuntu 10 and Fedora 12/13), and we've managed to track down one cause whilst investigating PR#14355. Some systems have Wine and hence the Wine symbol font installed. 'fontconfig', which is used by cairographics in X11(type='cairo') and many other applications, prefers the Wine symbol font to the standard Type 1 URW font, and seems to misinterpret its encoding. You may well have Wine installed without realizing it (as I did) -- it is increasingly common as a dependency of other software. The best test is to run % fc-match symbol s05l.pfb: Standard Symbols L Regular This is the result on a system without Wine: if you see % fc-match symbol symbol.ttf: Symbol Regular This seems to be the case with MacOS (10.6.4): $ uname -a Darwin lettu-2.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 $ fc-match symbol Symbol.ttf: Symbol 標準體 The X11(type = 'cairo') shows the problem with example(points); TestChars(font=5). However, there is no problem with the default device (quartz), nor with the default X11() which has type = 'Xlib' (unlike documented in ?X11: 'cairo' is available but 'Xlib' still used). What ever this is worth of (if this is worthless, I'll surely hear about it). Cheers, Jari Oksanen __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Aug 19, 2010, at 9:15 AM, Jari Oksanen wrote: The X11(type = 'cairo') shows the problem with example(points); TestChars(font=5). However, there is no problem with the default device (quartz), nor with the default X11() which has type = 'Xlib' (unlike documented in ?X11: 'cairo' is available but 'Xlib' still used). What ever this is worth of (if this is worthless, I'll surely hear about it). Well, maybe not worthless, but the X11 setup on Mac is poor in general. type=Xlib appears plainly not to work, and even disregarding the pi issue, the rotated y-axis labels come out pretty ugly. This is why quartz is now the default on OSX. BTW, it seems that the standard X11 Symbol,Regular font is simply absent on OSX. I can't get fc-match to list it, anyway. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Automatically retrieve correct collation
-Ursprüngliche Nachricht- Von: baptiste auguie [mailto:baptiste.aug...@googlemail.com] Gesendet: Donnerstag, 19. August 2010 07:41 An: Janko Thyson Cc: r-de...@r-project. org Betreff: Re: [Rd] Automatically retrieve correct collation Hi, roxygen can create the collate field for you, if you specify the dependencies in the commented code. I've never tested it with S4 classes though. HTH, baptiste Thanks Baptiste, I will have a look at Roxygen. Janko On 18 August 2010 22:28, Janko Thyson janko.thy...@ku-eichstaett.de wrote: Dear List, consider the following scenario: setClass(Class = A, representation = representation(B = B, C = C)) setClass(Class = B, representation = representation(C = C)) setClass(Class = C, representation = representation(something = character)) Obviously, the collation for sourcing these defs needs to be: C, B, A. Which doesn't correspond to the default collation of R (alphabetically). I've tried to pick up on how to ensure the right collation when building R Packages by reading some previous posts and as far as I understand I've basically got two options here: 1) Put all class defs in one script, e.g. allClasses.R. 2) Manually specify the collation via the Collate field in the DESCRIPTION file. I'm used to organizing my classes, generics, methods etc. on a one-per-script basis in various subdirectories (e.g. R/classes, R/methods etc.) and try automate manual steps wherever possible (not sure if that's the way most of you guys code, but it definitely helped me stay on top of things). But this doesn't really go well with my two options above, does it? ;-) So I thought about setting up a routine that - investigates the source code of all classes (via parsing and looking into the representation argument) - finds out the valid collation by itself based on all classes that it found in the representation argument of the respective class defs - and then writes all the class defs to one R script, e.g. allClasses.R, so I can bundle all my code in an R Package without worrying about the collation. This way I could stick to my old habits while automating the process of building a package a bit ;-) Now, I managed to get this done for simple class defs like the ones above but haven't looked into more complex class defs (e.g. including contains etc.) yet. Has anyone tried and succeeded in doing something similar or are all of you into the one-script-contains-all paradigm? If anyone is interested, I'd be glad to share code. Likewise I'd be interested in hearing about other best practices in this respect. Best regards, Janko __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr. Baptiste Auguié Departamento de Química Física, Universidade de Vigo, Campus Universitario, 36310, Vigo, Spain tel: +34 9868 18617 http://webs.uvigo.es/coloides __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] C or Java code generation
Hi All! I'm new to R and I need to know is it possible for R to generate C/C++ source code, Java byte code or native Win32 DLL like MatLab? --- WBR, Vyacheslav. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
Daniel Cegiełka пишет: http://www.rforge.net/r2c/ regards, daniel 2010/8/19 Vyacheslav Karamov ubuntul...@yandex.ru mailto:ubuntul...@yandex.ru Hi All! I'm new to R and I need to know is it possible for R to generate C/C++ source code, Java byte code or native Win32 DLL like MatLab? --- WBR, Vyacheslav. __ R-devel@r-project.org mailto:R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel Currently it is very experimantal and limited, intended for experiments with the language rather than real use __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
2010/8/19 Vyacheslav Karamov ubuntul...@yandex.ru Daniel CegieÅka пиÑеÑ: http://www.rforge.net/r2c/ regards, daniel 2010/8/19 Vyacheslav Karamov ubuntul...@yandex.ru mailto: ubuntul...@yandex.ru Hi All! I'm new to R and I need to know is it possible for R to generate C/C++ source code, Java byte code or native Win32 DLL like MatLab? --- WBR, Vyacheslav. __ R-devel@r-project.org mailto:R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel Currently it is very experimantal and limited, intended for experiments with the language rather than real use пÑивеÑÑÑвÑй ;) exactly http://www.dict.pl/dict?word=exactlylang=PL.. but Simon usually has high quality of code. regards, daniel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
Daniel Cegiełka пишет: 2010/8/19 Vyacheslav Karamov ubuntul...@yandex.ru mailto:ubuntul...@yandex.ru Daniel Cegiełka пишет: http://www.rforge.net/r2c/ regards, daniel 2010/8/19 Vyacheslav Karamov ubuntul...@yandex.ru mailto:ubuntul...@yandex.ru mailto:ubuntul...@yandex.ru mailto:ubuntul...@yandex.ru Hi All! I'm new to R and I need to know is it possible for R to generate C/C++ source code, Java byte code or native Win32 DLL like MatLab? --- WBR, Vyacheslav. __ R-devel@r-project.org mailto:R-devel@r-project.org mailto:R-devel@r-project.org mailto:R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel Currently it is very experimantal and limited, intended for experiments with the language rather than real use приветствуй ;) exactly http://www.dict.pl/dict?word=exactlylang=PL.. but Simon usually has high quality of code. regards, daniel Is there any posibility to use R without installing? I mean that I have my own application written in MS Visual C++ and I need to use R script in this app. I can install R and use it via DCOM, but it's not convenient for the end users of my program. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
Is there any posibility to use R without installing? I mean that I have my own application written in MS Visual C++ and I need to use R script in this app. I can install R and use it via DCOM, but it's not convenient for the end users of my program. Dirk Eddelbuettel love R/C++ combination. Rinside could be usefull for you. http://dirk.eddelbuettel.com/code.html regards [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Thu, 19 Aug 2010, peter dalgaard wrote: On Aug 19, 2010, at 9:15 AM, Jari Oksanen wrote: The X11(type = 'cairo') shows the problem with example(points); TestChars(font=5). However, there is no problem with the default device (quartz), nor with the default X11() which has type = 'Xlib' (unlike documented in ?X11: 'cairo' is available but 'Xlib' still used). What ever this is worth of (if this is worthless, I'll surely hear about it). Well, maybe not worthless, but the X11 setup on Mac is poor in general. type=Xlib appears plainly not to work, and even disregarding the pi issue, the rotated y-axis labels come out pretty ugly. This is why quartz is now the default on OSX. The even more serious issue under cairo of confusing style and weight is discussed on ?X11. BTW, it seems that the standard X11 Symbol,Regular font is simply absent on OSX. I can't get fc-match to list it, anyway. R's X11(type='cairo') device is using a version of cairographics compiled by Simon which includes a static build of fontconfig. So it is not really 'OSX'! I'm guessing you are using /usr/local/bin/fc-match which AFAIK also Simon's. It is also not using pango, and so not selecting fonts the same way as on Linux. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On 19/08/10 14:04 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: OSX. I can't get fc-match to list it, anyway. R's X11(type='cairo') device is using a version of cairographics compiled by Simon which includes a static build of fontconfig. So it is not really 'OSX'! I'm guessing you are using /usr/local/bin/fc-match which AFAIK also Simon's. $ which fc-match /usr/X11/bin/fc-match There seems to be no fc-match in /usr/local/bin/ in my Mac, so no Simon's utilities. (But this is, of course, pretty irrelevant for the main subject, and it seems that my installation of Ubuntu 10.04 is not affected by the problem but has quite regular fonts -- no Wine today. Better that I shut up). Cheers, Jari Oksanen It is also not using pango, and so not selecting fonts the same way as on Linux. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Thu, 2010-08-19 at 07:55 +0100, Prof Brian Ripley wrote: There have been spasmodic reports of symbols such as pi and infinity in plotmath being reproduced incorrectly on the X11 device on some Linux systems (at least Ubuntu 10 and Fedora 12/13), and we've managed to track down one cause whilst investigating PR#14355. Some systems have Wine and hence the Wine symbol font installed. 'fontconfig', which is used by cairographics in X11(type='cairo') and many other applications, prefers the Wine symbol font to the standard Type 1 URW font, and seems to misinterpret its encoding. You may well have Wine installed without realizing it (as I did) -- it is increasingly common as a dependency of other software. The best test is to run % fc-match symbol s05l.pfb: Standard Symbols L Regular This is the result on a system without Wine: if you see % fc-match symbol symbol.ttf: Symbol Regular you at least potentially have the problem. A good test is to look at ?points and run the function TestChars() defined there as TestChars(font=5) If you do have the problem, a workaround is to add the following lines to ~/.fonts.conf or /etc/fonts/local.conf (which you may need to create): match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match and repeat the fc-match test to check that it worked. Hi, I tried the suggested change to ~/.fonts.conf but am getting an error from fontconfig: $ fc-match symbol Fontconfig error: ~/.fonts.conf, line 10: junk after document element s05l.pfb: Standard Symbols L Regular $ cat ~/.fonts.conf match target=pattern test name=family stringSymbol/string /test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias I have an alias in there to solve the q symbol being used in Evince etc in place of pch == 1. Am I inserting this incorrectly? Many thanks, G (This workaround was culled from https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/551977 ) -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
If you have more than one element in a fonts.conf file you need to group them, e.g. fontconfig match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias /fontconfig On Thu, 19 Aug 2010, Gavin Simpson wrote: On Thu, 2010-08-19 at 07:55 +0100, Prof Brian Ripley wrote: There have been spasmodic reports of symbols such as pi and infinity in plotmath being reproduced incorrectly on the X11 device on some Linux systems (at least Ubuntu 10 and Fedora 12/13), and we've managed to track down one cause whilst investigating PR#14355. Some systems have Wine and hence the Wine symbol font installed. 'fontconfig', which is used by cairographics in X11(type='cairo') and many other applications, prefers the Wine symbol font to the standard Type 1 URW font, and seems to misinterpret its encoding. You may well have Wine installed without realizing it (as I did) -- it is increasingly common as a dependency of other software. The best test is to run % fc-match symbol s05l.pfb: Standard Symbols L Regular This is the result on a system without Wine: if you see % fc-match symbol symbol.ttf: Symbol Regular you at least potentially have the problem. A good test is to look at ?points and run the function TestChars() defined there as TestChars(font=5) If you do have the problem, a workaround is to add the following lines to ~/.fonts.conf or /etc/fonts/local.conf (which you may need to create): match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match and repeat the fc-match test to check that it worked. Hi, I tried the suggested change to ~/.fonts.conf but am getting an error from fontconfig: $ fc-match symbol Fontconfig error: ~/.fonts.conf, line 10: junk after document element s05l.pfb: Standard Symbols L Regular $ cat ~/.fonts.conf match target=pattern test name=family stringSymbol/string /test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias I have an alias in there to solve the q symbol being used in Evince etc in place of pch == 1. Am I inserting this incorrectly? Many thanks, G (This workaround was culled from https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/551977 ) -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Thu, 2010-08-19 at 12:36 +0100, Prof Brian Ripley wrote: If you have more than one element in a fonts.conf file you need to group them, e.g. Many thanks, Prof. Ripley. That is working just fine now on my Fedora 12 workstation. All the best, G fontconfig match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias /fontconfig On Thu, 19 Aug 2010, Gavin Simpson wrote: On Thu, 2010-08-19 at 07:55 +0100, Prof Brian Ripley wrote: There have been spasmodic reports of symbols such as pi and infinity in plotmath being reproduced incorrectly on the X11 device on some Linux systems (at least Ubuntu 10 and Fedora 12/13), and we've managed to track down one cause whilst investigating PR#14355. Some systems have Wine and hence the Wine symbol font installed. 'fontconfig', which is used by cairographics in X11(type='cairo') and many other applications, prefers the Wine symbol font to the standard Type 1 URW font, and seems to misinterpret its encoding. You may well have Wine installed without realizing it (as I did) -- it is increasingly common as a dependency of other software. The best test is to run % fc-match symbol s05l.pfb: Standard Symbols L Regular This is the result on a system without Wine: if you see % fc-match symbol symbol.ttf: Symbol Regular you at least potentially have the problem. A good test is to look at ?points and run the function TestChars() defined there as TestChars(font=5) If you do have the problem, a workaround is to add the following lines to ~/.fonts.conf or /etc/fonts/local.conf (which you may need to create): match target=pattern test name=familystringSymbol/string/test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match and repeat the fc-match test to check that it worked. Hi, I tried the suggested change to ~/.fonts.conf but am getting an error from fontconfig: $ fc-match symbol Fontconfig error: ~/.fonts.conf, line 10: junk after document element s05l.pfb: Standard Symbols L Regular $ cat ~/.fonts.conf match target=pattern test name=family stringSymbol/string /test edit name=family mode=prepend binding=same stringStandard Symbols L/string /edit /match alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias I have an alias in there to solve the q symbol being used in Evince etc in place of pch == 1. Am I inserting this incorrectly? Many thanks, G (This workaround was culled from https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/551977 ) -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Aug 19, 2010, at 1:04 PM, Prof Brian Ripley wrote: On Thu, 19 Aug 2010, peter dalgaard wrote: On Aug 19, 2010, at 9:15 AM, Jari Oksanen wrote: The X11(type = 'cairo') shows the problem with example(points); TestChars(font=5). However, there is no problem with the default device (quartz), nor with the default X11() which has type = 'Xlib' (unlike documented in ?X11: 'cairo' is available but 'Xlib' still used). What ever this is worth of (if this is worthless, I'll surely hear about it). Well, maybe not worthless, but the X11 setup on Mac is poor in general. type=Xlib appears plainly not to work, and even disregarding the pi issue, the rotated y-axis labels come out pretty ugly. This is why quartz is now the default on OSX. The even more serious issue under cairo of confusing style and weight is discussed on ?X11. BTW, it seems that the standard X11 Symbol,Regular font is simply absent on OSX. I can't get fc-match to list it, anyway. R's X11(type='cairo') device is using a version of cairographics compiled by Simon which includes a static build of fontconfig. So it is not really 'OSX'! I'm guessing you are using /usr/local/bin/fc-match which AFAIK also Simon's. Actually, it was /opt/local/bin/fc-match (macPorts?). I have _three_ of them: peter-dalgaards-iMac:~ pd$ ls -l /usr/X11/bin/fc-match -rwxr-xr-x 1 root wheel 64416 Feb 11 2010 /usr/X11/bin/fc-match peter-dalgaards-iMac:~ pd$ ls -l /usr/local/bin/fc-match -rwxr-xr-x@ 1 root wheel 1476560 Oct 21 2008 /usr/local/bin/fc-match peter-dalgaards-iMac:~ pd$ ls -l /opt/local/bin/fc-match -rwxr-xr-x 2 root admin 14792 Mar 16 16:52 /opt/local/bin/fc-match Doesn't look like they are behaving any different, though. It is also not using pango, and so not selecting fonts the same way as on Linux. You're assuming (in fact, correctly) that I was using Simon's build, but my locally built version is similar. That doesn't appear to use pango either; I have a Portfile for pango-devel, but it must have failed to build. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] One possible cause for incorrect symbols in X11() output
On Aug 19, 2010, at 1:55 PM, peter dalgaard wrote: It is also not using pango, and so not selecting fonts the same way as on Linux. You're assuming (in fact, correctly) that I was using Simon's build, but my locally built version is similar. That doesn't appear to use pango either; I have a Portfile for pango-devel, but it must have failed to build. Actually, it builds, but the resulting R crashes on x11();plot(0) -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
On 19 August 2010 at 13:02, Daniel Cegiełka wrote: | Is there any posibility to use R without installing? | | I mean that I have my own application written in MS Visual C++ and I need | to use R script in this app. I can install R and use it via DCOM, but it's | not convenient for the end users of my program. | | | Dirk Eddelbuettel love R/C++ combination. Rinside could be usefull for you. | | http://dirk.eddelbuettel.com/code.html Thanks for the plug. We can definitely embed R inside C++ on operating systems containing an x somewhere in their name. But note that the RInside page (http://dirk.eddelbuettel.com/code/rinside.html) clearly states the following: Status Version 0.2.3 should build and install on just about any Linux and OS X system, and even on Windows machines that have the Rtools compiled by Duncan Murdoch as detailed in the The Windows Toolset appendix to the R Installation manual. Do not report an error if you fail to build this with another compiler as this is not supported. (However, the examples which built and run under 0.2.1 currently build but segfault. This is probably fixable but we just haven't had the time or focus to do it. Linux and OS X work well enough for us.) so for someone hell-bent on using MS Visual Whatever this is not a solution. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] c.POSIXct
I used to get caught by this c() behaviour often, but now I do expect it to
drop attributes. I think it would break many things if you change it, and force
people to write different code when they really do want to drop attributes.
When you want new behaviour it is usually better to define a new function, ca()
maybe?
Paul
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-
project.org] On Behalf Of Gabor Grothendieck
Sent: August 18, 2010 6:23 PM
To: r-devel@r-project.org
Subject: Re: [Rd] c.POSIXct
No one answered this so I submitted it to the bugs system and there I
got the response that it is documented behavior; however, whether its
documented or not is hardly the point -- its undesirable that tzone is
lost when using c.
On Thu, Aug 12, 2010 at 11:33 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
Currently if x1 and x2 are POSIXct then c(x1, x2) will not have a
tzone attribute even if x1 or x2 or both do but it should.
This could be fixed with the following c.POSIXct:
c.POSIXct - function (..., recursive = FALSE) {
tzones - lapply(list(...), attr, which = tzone)
lengths - sapply(tzones, length)
if (any(lengths 1)) stop(tzone cannot have length greater
than 1)
which - sapply(tzones, length) == 1
tzone - unique(unlist(tzones[which]))
if (length(tzone) != 1) tzone - NULL
structure(c(unlist(lapply(list(...), unclass))), class = c(POSIXt,
POSIXct), tzone = tzone)
}
# test
x1 - Sys.time()
x2 - structure(x1, tzone = UTC)
x3 - structure(x1, tzone = other)
# these all currently give NULL but with
# above give indicated value
attr(c(x1, x1), tzone) # NULL
attr(c(x2, x2), tzone) # UTC
attr(c(x1, x2), tzone) # UTC
attr(c(x2, x1), tzone) # UTC
attr(c(x1, x2, x3), tzone) # NULL
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Re: [Rd] c.POSIXct
On Thu, Aug 19, 2010 at 10:16 AM, Paul Gilbert pgilb...@bank-banque-canada.ca wrote: I used to get caught by this c() behaviour often, but now I do expect it to drop attributes. I think it would break many things if you change it, and force people to write different code when they really do want to drop attributes. When you want new behaviour it is usually better to define a new function, ca() maybe? That would work if ca defaulted to c for those classes that did not supply a ca method. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] c.POSIXct
Hi, Gabor, Paul, et al.: For classes that did not supply a ca method, I'd rather see the default being to start with the corresponding c method followed by an effort to preserve attributes to the maximum extent feasible. I'm not sure the best defaults, but at the moment, I would expect that attributes like dim and dimnames should always be dropped. The current default c method preserves names appropriately. What do you think about including another argument to checkAttributes? I'm not sure what the options should be nor what should be the default, but one option should throw and error if any contradiction was found while another would take all attributes from the first argument and ignore others. Best Wishes, Spencer Graves On 8/19/2010 7:32 AM, Gabor Grothendieck wrote: On Thu, Aug 19, 2010 at 10:16 AM, Paul Gilbert pgilb...@bank-banque-canada.ca wrote: I used to get caught by this c() behaviour often, but now I do expect it to drop attributes. I think it would break many things if you change it, and force people to write different code when they really do want to drop attributes. When you want new behaviour it is usually better to define a new function, ca() maybe? That would work if ca defaulted to c for those classes that did not supply a ca method. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C or Java code generation
On 19 August 2010 at 17:06, Vyacheslav Karamov wrote: | Dirk Eddelbuettel пишет: | On 19 August 2010 at 13:02, Daniel Cegiełka wrote: | | Is there any posibility to use R without installing? | | | | I mean that I have my own application written in MS Visual C++ and I need | | to use R script in this app. I can install R and use it via DCOM, but it's | | not convenient for the end users of my program. | | | | | | Dirk Eddelbuettel love R/C++ combination. Rinside could be usefull for you. | | | | http://dirk.eddelbuettel.com/code.html | | Thanks for the plug. We can definitely embed R inside C++ on operating | systems containing an x somewhere in their name. But note that the RInside | page (http://dirk.eddelbuettel.com/code/rinside.html) clearly states the | following: | | Status | | Version 0.2.3 should build and install on just about any Linux and OS X | system, and even on Windows machines that have the Rtools compiled by | Duncan Murdoch as detailed in the The Windows Toolset appendix to the R | Installation manual. Do not report an error if you fail to build this with | another compiler as this is not supported. (However, the examples which | built and run under 0.2.1 currently build but segfault. This is probably | fixable but we just haven't had the time or focus to do it. Linux and OS X | work well enough for us.) | | so for someone hell-bent on using MS Visual Whatever this is not a solution. | | Dirk | | | I tried to compile it using MinGW: No, what you describe in the next few hundred lines would _build the examples if the package is already installed_ Also, building these examples (once you have the package is installed) does Work For Me (TM) in the sense that the compiles and linking steps succeed (WinXP, Rtools with gcc/g++ 4.2.x, R 2.11.0) yet it, as noted above, leads to a seg.fault which Romain and I have found neither time nor motivation to fix. You would be very welcome to help out -- our discussions around Rcpp and RInside take place on the rcpp-devel list off R-Forge. | 1) First I added R_HOME environment variable. | 2) Then modified c:\Program | Files\R\R-2.11.1\library\RInside\examples\standard\Makefile.win by | surrounding $(R_HOME)/bin/R with the quotation marks. | 3) And finally | C:\Program Files\R\R-2.11.1\library\RInside\examples\standardmake -f | Makefile.win | g++ -Ic:/PROGRA~1/R/R-211~1.1/include | -Ic:/PROGRA~1/R/R-211~1.1/library/Rcpp/include | -Ic:/PROGRA~1/R/R-211~1.1/library/RInside/include -O2 -Wall -Wall -s | rinside_callbacks0.cpp -Lc:/PROGRA~1/R/R-211~1.1/bin -lR | -Lc:/PROGRA~1/R/R-211~1.1/bin -lRblas -Lc:/PROGRA~1/R/R-211~1.1/bin | -lRlapack c:/PROGRA~1/R/R-211~1.1/library/RInside/lib/libRInside.a | c:/PROGRA~1/R/R-211~1.1/library/Rcpp/lib/libRcpp.a -o rinside_callbacks0 | c:/PROGRA~1/R/R-211~1.1/library/RInside/lib/libRInside.a(RInside.o):RInside.cpp:(.text+0x10b): | undefined reference to `__gxx_personality_sj0' [ Hundreds of similar lines removed. ] Thanks, Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] perl.exe has stopped working: Fixed.
To complete this thread for anyone encountering a similar problem, the fix I said I'd try (below) worked. Specifically, I installed the latest Strawberry Perl, modified the path so the first reference points to the new Perl, and R CMD build, check, INSTALL, and INSTALL -build all seemed to work properly. Of course, there is always a chance of some deeply hidden problem, but the obvious first tests seemed to function exactly as I have come to expect. Best Wishes, Spencer Graves On 8/18/2010 6:00 PM, Spencer Graves wrote: Hello: I just installed 14 security updates for Vista x64, and now R CMD build packagename terminates, saying, perl.exe has stopped working. I reinstalled Rtools211 using the latest version after uninstalling the version I installed on 4/3/2010. What do you suggest? I can install the latest version of perl from www.perl.org (5.12.1), but I thought I'd ask here first. Thanks, Best Wishes, Spencer Graves __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Can you share a working example of R program aided by fast BLAS?
Can one of you give me an R program that displays the benefits an accelerated BLAS in R? Here's why I ask, in case you wonder: In a linux cluster, I've hit some bumps in the road. The worst one by far was that I installed R, then GotoBLAS2 with default settings, and after that, jobs using Rmpi were *really* *really* slow. I mean horrible. If a job took 15 minutes when run by itself, outside of MPI, it took 1 full day when run inside MPI. Literally the same job. I learned later that GotoBLAS2 defaults to allow threads equal to the number of cores, and that the threads are not compatible with MPI. This latter point not clearly stated in the GotoBLAS2 documents, so far as I can find, but after I realized that was the problem, I did find one other cluster website that mentioned the same problem. If your application uses GotoBLAS and all cores as MPI threads, setting GOTO_NUM_THREADS larger than one will usually result in drastically slower performance. (http://hpc.uark.edu/hpc/support/software/numerical.html#gotoblas). In the GotoBLAS2 documentation, it warns of weird thread related delays, but it implies that the slowdown--if it happens--is a result of bad user code, rather than this more fundamental mismatch between OpenMPI (or MPI in general) and GotoBLAS2. In the process of diagnosing the big slowdown, I've been making many time comparisons. When I installed GotoBLAS2 in the first place, it was because so many people (and the R admin manual) said that R's ordinary BLAS is rudimentary/slow. In the test cases I've tried, R's BLAS is not that bad. In fact, in the test programs we run, the time is not substantially different with GotoBLAS2 and R's BLAS. I also compared the Intel Kernel Math Library BLAS and didn't notice a huge difference. So, well, I think that means I'm running bad test cases for R and GotoBLAS2. Oh, and one more thing. I have not been able to find an example R program that benefitted at all from allowing threads 1 in GotoBLAS2 environment settings. In fact, if a one-thread job takes15 minutes, the one that allows 2 or more threads is 21 minutes. And the more threads allowed causes a job to take longer. This is literally the same job, same cluster node, the only difference is changing the environment variable that adjusts the GotoBLAS2 threads allowed. So if you know whether your example depends on threads or not, I would appreciate the warning. pj -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... Thanks and regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I have read a significant number of vignettes from Bioconductor packages and I have never seen it used. Kasper On Thu, Aug 19, 2010 at 3:17 PM, Marc Schwartz marc_schwa...@me.com wrote: On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... Thanks and regards, Marc Schwartz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 3:17 PM, Marc Schwartz wrote: On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error. For example, currently you get this: Error: chunk 1 (label=named) Error in parse(text = chunk) : unexpected symbol in x - foo bar Execution halted and I'd like errors to be more like this: Error: chunk 1 (label=named) Error in parse(text = chunk, srcfile = srcfile) : test.Rnw:9:10: unexpected symbol 9: x - foo bar ^ Execution halted It turns out that this requires changes that make the expand=FALSE option quite hard to implement. Is anyone using it? For those who don't know it, expand=FALSE means that a code chunk like echo=TRUE, keep.source=TRUE,expand=FALSE= z - 3 named @ will be displayed as z - 3 named rather than expanding the named chunk. I'd like to drop the option, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch I don't. So 1 go ahead and drop it vote... You may want to post this to R-Help though Duncan, as I suspect there may be more Sweave users there than here... I probably will before I go ahead with this, but I may as well start on this group. Duncan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I never used it. I got curious, though. What would be a situation that benefits of this option? Maybe a use case could be found by brute force (grep all .Rnw files on CRAN for the option? Claudia -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 4:29 PM, Claudia Beleites wrote: I never used it. I got curious, though. What would be a situation that benefits of this option? When I put it in, I thought it would be for people who were writing about Sweave. Duncan Murdoch Maybe a use case could be found by brute force (grep all .Rnw files on CRAN for the option? Claudia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 5:07 PM, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
Okay, thanks. I'll keep it in. So now I have a question: suppose
you have an error (syntax error at this point, maybe some other kinds of
error in the future) in the getInfoAboutThisSample chunk, but that
chunk wasn't eval'd, mainloop was eval'd. So the error is going to be
reported as occurring in chunk mainloop, but with a line number from
somewhere else in the file. Is that a problem?
Duncan Murdoch
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
I picked the example from segmenting chromosomes for a reason. I have a
fair chunk of code that deals with not quite exceeding the amount of RAM
available in the machine sitting on my desktop. If I use functions,
then the pass-by-value semantics of R will push me beyond the limits at
some points. (This is an empirical statement, not a theoretical one. I
was bitten by it several times while trying to analyze a couple of these
datasets. And, yes, I know I can get around this by buying a bigger and
better machine; it's on order...) The real point is that using
functions can be detrimental to the efficiency of the program, in ways
that have real world consequences.
I haven't thought about doing the same thing with expressions.
Expressions don't have quite the same semantics as chunks, and you'd
have to make sure the evaluation was delayed so that you cold use the
current values of things that were computed in the meantime and I
already know how to do this with chunks without having to think so hard.
Using expressons would, however, help with the one difficulty that I
have with reusing chunks (independent of whether or not I use
'expand=FALSE'). I usually work inside emacs, using the
emacs-speaks-statistics (ESS) package. ESS doesn't know how to evaluate
the chunk call inside another chunk. so if I want to step through
the code during development, I have to jump around myself to locate the
source chunks. With expressions that wouldn't matter.
As I ramble on about this, it occurs to me that the underlying issue is
that chunks are not first class objects either in the LaTeX world or
in the R world part of Sweave. If there were a way to promote them to
first class objects somehow, then it might make my use of ESS easier
while simultaneously making it easier for Duncan to figure out how to
report the correct line numbers. But I only have an extremely vague
idea of how one might start to do that...
Kevin
Matt Shotwell wrote:
On Thu, 2010-08-19 at 17:07 -0400, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
Couldn't you achieve the same amount of abstraction using function
calls, rather than embedded code chunks? The reader can then see real
code, rather than non-code, or meta-code, or whatever. Alternatively,
represent the code chunks as R expressions, then evaluate the
expressions at the appropriate points.
-Matt
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Thu, Aug 19, 2010 at 6:21 PM, Kevin Coombes kevin.r.coom...@gmail.com wrote: I picked the example from segmenting chromosomes for a reason. I have a fair chunk of code that deals with not quite exceeding the amount of RAM available in the machine sitting on my desktop. If I use functions, then the pass-by-value semantics of R will push me beyond the limits at some points. (This is an empirical statement, not a theoretical one. I was bitten by it several times while trying to analyze a couple of these datasets. And, yes, I know I can get around this by buying a bigger and better machine; it's on order...) The real point is that using functions can be detrimental to the efficiency of the program, in ways that have real world consequences. I haven't thought about doing the same thing with expressions. Expressions don't have quite the same semantics as chunks, and you'd have to make sure the evaluation was delayed so that you cold use the current values of things that were computed in the meantime and I already know how to do this with chunks without having to think so hard. Using expressons would, however, help with the one difficulty that I have with reusing chunks (independent of whether or not I use 'expand=FALSE'). I usually work inside emacs, using the emacs-speaks-statistics (ESS) package. ESS doesn't know how to evaluate the chunk call inside another chunk. so if I want to step through the code during development, I have to jump around myself to locate the source chunks. With expressions that wouldn't matter. As I ramble on about this, it occurs to me that the underlying issue is that chunks are not first class objects either in the LaTeX world or in the R world part of Sweave. If there were a way to promote them to first class objects somehow, then it might make my use of ESS easier while simultaneously making it easier for Duncan to figure out how to report the correct line numbers. But I only have an extremely vague idea of how one might start to do that... You could try a macro instead and see how it performs. There is an article by Thomas Lumley in R News 2003-1 and an implementation in the gtools package. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] No RTFM?
What do you think about adding a No RTFM policy to the R mailing
lists? Per, http://en.wikipedia.org/wiki/RTFM:
The Ubuntu Forums and LinuxQuestions.org, for instance, have instituted
no RTFM policies to promote a welcoming atmosphere.[8][9].
RTFM [and] Go look on google are two inappropriate responses to a
question. If you don't know the answer or don't wish to help, please say
nothing instead of brushing off someone's question. Politely showing
someone how you searched or obtained the answer to a question is
acceptable, even encouraged.
...
If you wish to remind a user to use search tools or other resources when
they have asked a question you feel is basic or common, please be very
polite. Any replies for help that contain language disrespectful towards
the user asking the question, i.e. STFU or RTFM are unacceptable and
will not be tolerated. —Ubuntu Forums
Gavin Simpson and I recently provided examples answering a question from
r.ookie that had previously elicited responses, You want us to read
the help page to you? and It yet again appears that you are asking us
to read the help pages for you.
I can appreciate the sentiment in fortunes('rtfm'). In this case,
however, r.ookie had RTFM (and said so), but evidently the manual was
not sufficiently clear.
Best Wishes,
Spencer Graves
__
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Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On Thu, 19 Aug 2010, Kevin Coombes wrote:
I picked the example from segmenting chromosomes for a reason. I have a fair
chunk of code that deals with not quite exceeding the amount of RAM available
in the machine sitting on my desktop. If I use functions, then the
pass-by-value semantics of R will push me beyond the limits at some points.
(This is an empirical statement, not a theoretical one. I was bitten by it
several times while trying to analyze a couple of these datasets. And, yes, I
know I can get around this by buying a bigger and better machine; it's on
order...) The real point is that using functions can be detrimental to the
efficiency of the program, in ways that have real world consequences.
I haven't thought about doing the same thing with expressions. Expressions
don't have quite the same semantics as chunks, and you'd have to make sure
the evaluation was delayed so that you cold use the current values of things
that were computed in the meantime and I already know how to do this with
chunks without having to think so hard.
Using expressons would, however, help with the one difficulty that I have
with reusing chunks (independent of whether or not I use 'expand=FALSE').
I usually work inside emacs, using the emacs-speaks-statistics (ESS) package.
ESS doesn't know how to evaluate the chunk call inside another chunk. so
if I want to step through the code during development, I have to jump around
myself to locate the source chunks. With expressions that wouldn't matter.
emacs org-mode might help.
You can define a chunk, ch1 (say), then place it in a subsequent
chunk, ch2 (say), inside an eval() and refer to ch2 inside an
eval() inside another chunk, ch3, and so on. The only trick is to
write the chunk so that the chunk it refers to is on its own line, like
this:
#+source: ch3
#+begin_src R :session :noweb yes
eval(
ch2
)
z - mean(y)+1
#+end_src
as the noweb expansion will repeat any other text on the line with the
named chunk for each line of code in the referenced chunk.
You can define a library of chunks separately, which might help you if you
reuse them in different places.
You can use ess-mode to edit the chunks and execute them with the usual
ess-eval-* commands, or run them in org-mode with the results optionally
returned to the edit buffer, but outside the code block.
If you want to debug a bunch of nested chunks and 'step through the code
during development', you can tangle the chunk you wish to execute to
produce a *.R file. The nested chunks are expanded into R. Open that *.R
file and debug away.
With a recent emacs, I think this gets you going:
C-h i m Org Mode RET C-s source RET RET
or Google 'org-babel R' or some such or just go look here:
http://blogisticreflections.wordpress.com/
As I ramble on about this, it occurs to me that the underlying issue is that
chunks are not first class objects either in the LaTeX world or in the R
world part of Sweave. If there were a way to promote them to first class
objects somehow, then it might make my use of ESS easier while simultaneously
making it easier for Duncan to figure out how to report the correct line
numbers. But I only have an extremely vague idea of how one might start to
do that...
org-mode might be the path of least resistance.
FWIW, the code chunks are objects processed by emacs-lisp before they are
handed off to R, so there might be a slicker way to handle the nesting
than dropping chunks inside eval()s in R blocks. If that interests you,
there is a very active listserv for orgmode, where you might inqure.
HTH,
Chuck
Kevin
Matt Shotwell wrote:
On Thu, 2010-08-19 at 17:07 -0400, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of
code.
Couldn't you achieve the same amount of abstraction using function
