[Rd] Using SVN + SSH on windows
Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
From my memory: I guess you need to tell TortoiseSVN to use plink as your ssh client. I do not use putty myself hence cannot look into the details here. Uwe Ligges On 27.03.2010 15:12, Christophe Genolini wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ 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] Using SVN + SSH on windows
On Sat, Mar 27, 2010 at 3:12 PM, Christophe Genolini cgeno...@u-paris10.fr wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. All looks ok, but I think you are using the wrong protocol. It should be 'svn+ssh' for *commits*, i.e. svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d which *is* shown at http://r-forge.r-project.org/scm/?group_id=727 /Henrik PS. Don't think you need plink, but I might be wrong. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ 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] Using SVN + SSH on windows
2010/3/27 hb h...@stat.berkeley.edu: On Sat, Mar 27, 2010 at 3:12 PM, Christophe Genolini cgeno...@u-paris10.fr wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. All looks ok, but I think you are using the wrong protocol. It should be 'svn+ssh' for *commits*, i.e. svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d which *is* shown at http://r-forge.r-project.org/scm/?group_id=727 Sorry, I missed that you've tried that (I scrolled past it on my small screen). - When you generated a key in PUTTYgen, did you enter a passphrase? I think you have to leave that blank. - Make sure not to have any newlines/spaces in the key, when you paste it, that is, you should have: Line 1: ssh-rsa Line 2: long key You can have multiple entries as the above. - You need to checkout with the svn+ssh URL, because that it is what TortoiseSVN will use for commits (unless you do relocate). If you can checkout using this protocol, you should be able to commit. Thus, focus your troubleshooting on checking out. - In the Default Settings PuTTY Configurations, make sure Attempt authentication using Pageant is checked under the Connection - SSH - Auth panel. - Make sure Pageant lists the key in its dialog. Does it work? /Henrik /Henrik PS. Don't think you need plink, but I might be wrong. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ 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] Using SVN + SSH on windows
Henrik Bengtsson a écrit : 2010/3/27 hb h...@stat.berkeley.edu: On Sat, Mar 27, 2010 at 3:12 PM, Christophe Genolini cgeno...@u-paris10.fr wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. All looks ok, but I think you are using the wrong protocol. It should be 'svn+ssh' for *commits*, i.e. svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d which *is* shown at http://r-forge.r-project.org/scm/?group_id=727 Now, in addition, I configure putty as Uwe advice me. I follow the tutorial http://www.mono-project.com/Putty_and_TortoiseSvn Sorry, I missed that you've tried that (I scrolled past it on my small screen). - When you generated a key in PUTTYgen, did you enter a passphrase? I think you have to leave that blank. - Make sure not to have any newlines/spaces in the key, when you paste it, that is, you should have: Line 1: ssh-rsa Line 2: long key On two line ? On R-forge, they say /Make sure there are no line breaks except between keys./ You can have multiple entries as the above. - You need to checkout with the svn+ssh URL, because that it is what TortoiseSVN will use for commits (unless you do relocate). If you can checkout using this protocol, you should be able to commit. Thus, focus your troubleshooting on checking out. - In the Default Settings PuTTY Configurations, make sure Attempt authentication using Pageant is checked under the Connection - SSH - Auth panel. I did - Make sure Pageant lists the key in its dialog. It is. Does it work? No. In putty, I get : login as: christophe Then a pop up say : Assertion failed! Program:...\pageant.exe File: ..\sshrsa.c Line:793 ... Then I click ignore On putty again : Authenticating with public key rsa-key-20100327 from agent Access denied christo...@kml3d.r-forge.r-project.org's password: Linux xmrforge2 2.6.18-xen #1 SMP Fri May 18 16:01:42 BST 2007 x86_64 The programs included with the Debian GNU/Linux system are free software; the exact distribution terms for each program are described in the individual files in /usr/share/doc/*/copyright. Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent permitted by applicable law. Last login: Sat Mar 27 17:56:55 2010 from def92-4-82-225-59-146.fbx.proxad.net This is a restricted account. You cannot execute anything here. Goodbye. /Henrik /Henrik PS. Don't think you need plink, but I might be wrong. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ 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] Using SVN + SSH on windows
I am using TortoiseSVN 1.6.7 on Vista and right clicking in Windows explorer and choosing TortoiseSVN | TortoiseSVN Settings | Network gives a blank dialog. In fact I don't think I have ever used the TortoiseSVN Network dialog at all yet I am able to use TortoiseSVN to send commits to R-Forge. Not sure it matters but I normally run pageant from the command line like this: pageant \mydir\privatekey.ppk I also had a lot of problems getting commits to R-Forge to work from Windows. The entire system is really geared to UNIX. It took me a couple of days of trial and error (since you have to wait 20 minutes for each try) before I got it working. Although I did get it to work, I ultimately decided to host all my packages on googlecode. googlecode is extremely easy to use from Windows and does not require any public/private key, pageant, etc. e.g. http://sqldf.googlecode.com. If you already have TortoiseSVN and know how to use it then you can probably set up a googlecode site in literally 5 minutes. One other possibility. I think there is a way to host your project on googlecode but still have it mirrored on R-forge so from your users' viewpoint its the same as if it were on R-Forge but you can use the simpler googlecode site. In that case you might not need to set up commits on R-Forge since you would do all your commits through googlecode (depending on how it works) but I have not seen good documentation on how to do this. 2010/3/27 Uwe Ligges lig...@statistik.tu-dortmund.de: From my memory: I guess you need to tell TortoiseSVN to use plink as your ssh client. I do not use putty myself hence cannot look into the details here. Uwe Ligges On 27.03.2010 15:12, Christophe Genolini wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
It is really not hard to set it up. I am using a vanilla ssh (rather than putty) and that works fine all the time... Uwe Ligges On 27.03.2010 18:31, Gabor Grothendieck wrote: s getting commits to R-Forge to work from Windows. The entire system is really geared to UNIX. It took me a couple of days of trial and error (since you have to wait 20 minutes for each try) before I got it working. Although I did get it to work, I ultimately decided to host all my packages on googlecode. googlecode is extremely easy to use from Windows and does not require any public/private key, pageant, etc. e.g. http://sqldf.googlecode.com. If you already have TortoiseSVN and know how to use it then you can probably set up a googlecode site in literally 5 minutes. One other possibility. I think there is a way to host your project on googlecode but still have it mirrored on R-forge so from your users' viewpoint its the same as if it were on R-Forge but you can use the simpler googlecode site. In that case you might not need to set up commits on R-Forge since you would do all your commits through googlecode (depending on how it works) but I have not seen good documentation on how to do this. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
The worst part is the 20 minute delay which means that if here is something wrong and you don't know what it is and need to try various things via trial and error each try takes 20 minutes so its not surprising that it can be extremely time consuming to set up. I did set it up a long time ago so perhaps the situation is better now but my experience at the time was more like Christophe's. If the 20 minute turnaround cannot be solved then I think the best solution for Windows users would be excellent step by step documentation on how to mirror your repository onto R-Forge from googlecode and elsewhere so that Windows users can do their commits on googlecode (assuming that mirroring your repository is possible and is easier than the commit procedure and does not involve the 20 minute delay). 2010/3/27 Uwe Ligges lig...@statistik.tu-dortmund.de: It is really not hard to set it up. I am using a vanilla ssh (rather than putty) and that works fine all the time... Uwe Ligges On 27.03.2010 18:31, Gabor Grothendieck wrote: s getting commits to R-Forge to work from Windows. The entire system is really geared to UNIX. It took me a couple of days of trial and error (since you have to wait 20 minutes for each try) before I got it working. Although I did get it to work, I ultimately decided to host all my packages on googlecode. googlecode is extremely easy to use from Windows and does not require any public/private key, pageant, etc. e.g. http://sqldf.googlecode.com. If you already have TortoiseSVN and know how to use it then you can probably set up a googlecode site in literally 5 minutes. One other possibility. I think there is a way to host your project on googlecode but still have it mirrored on R-forge so from your users' viewpoint its the same as if it were on R-Forge but you can use the simpler googlecode site. In that case you might not need to set up commits on R-Forge since you would do all your commits through googlecode (depending on how it works) but I have not seen good documentation on how to do this. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Installing R-packages in Windows Using Rtools - compilation error when signal.h included in C header
Hi all, I have been attempting to find a resolution to this problem but could not to any avail. I am attempting to install an R-package from source in windows that depends on underlying C-code. I should mention that this error is not found when installing this package from source in Linux or Mac. To do this I have installed R-tools 2.11 and was successfully able to use R and basic unix commands from the windows command prompt. When I install my package from the windows command prompt with R CMD INSTALL packagename however, the C files within the source directory all compiles until it hits a file called cheapcgi.c, where the following error is given: gcc -Ic:/R/include -O3 -Wall -std=gnu99 -c cheapcgi.c -o cheapcgi.o cheapcgi.c: In function 'catchSignal': cheapcgi.c:538: error: 'SIGBUS' undeclared (first use in this function) cheapcgi.c:538: error: (Each undeclared identifier is reported only once cheapcgi.c:538: error: for each function it appears in.) cheapcgi.c:546: error: 'SIGKILL' undeclared (first use in this function) cheapcgi.c: In function 'initSigHandlers': cheapcgi.c:558: error: 'SIGBUS' undeclared (first use in this function) make: *** [cheapcgi.o] Error 1 ... done ERROR: compilation failed for package 'zinba' * removing 'c:/R/library/zinba' Exploring this error further, I see these variables are defined in the standard C header file signal.h, and is linked to in cheapcgi.c using #include signal.h in the beginning of the file. Now, the other C files have compiled successfully before reaching this file, so I know that the MinGW compiler is at least working. When checking the mingw/include directory in the Rtools folder, I do indeed see a file for signal.h, so it is not missing. This problem is baffling and I could not find any documents talking about this issues online. I do realize that system signals may not work in windows, but at least the header files for the signal.h should be found. I would be greatly appreciative if anyone can shed any insight on this issue. Again, this is only when installing R packages in windows using Rtools, not in Mac or Linux. Thanks very much, Naim __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
On 27 March 2010 at 13:50, Gabor Grothendieck wrote: | The worst part is the 20 minute delay which means that if here is | something wrong and you don't know what it is and need to try various | things via trial and error each try takes 20 minutes so its not | surprising that it can be extremely time consuming to set up. I did | set it up a long time ago so perhaps the situation is better now but | my experience at the time was more like Christophe's. If the 20 | minute turnaround cannot be solved then I think the best solution for | Windows users would be excellent step by step documentation on how to | mirror your repository onto R-Forge from googlecode and elsewhere so | that Windows users can do their commits on googlecode (assuming that | mirroring your repository is possible and is easier than the commit | procedure and does not involve the 20 minute delay). I think you are being rather unfair here. These are contributed service being provided by folks in their extra time that they could be spending for their own work or research instead. The general rule still is: stop complaining, and volunteer to provide something that is better (or at least write the aforementioned step-by-step tutorial). Otherwise you are just making noise with no signal whatsoever. R-Forge is a rocksolid service for hundreds of us, and (at least the folks I work with) are very appreciative of the service. So a big Thank You from my end. Dirk | 2010/3/27 Uwe Ligges lig...@statistik.tu-dortmund.de: | It is really not hard to set it up. I am using a vanilla ssh (rather than | putty) and that works fine all the time... | | Uwe Ligges | | | On 27.03.2010 18:31, Gabor Grothendieck wrote: | | s getting commits to R-Forge to work from | Windows. The entire system is really geared to UNIX. It took me a | couple of days of trial and error (since you have to wait 20 minutes | for each try) before I got it working. Although I did get it to work, | I ultimately decided to host all my packages on googlecode. | googlecode is extremely easy to use from Windows and does not require | any public/private key, pageant, etc. e.g. | http://sqldf.googlecode.com. If you already have TortoiseSVN and know | how to use it then you can probably set up a googlecode site in | literally 5 minutes. | | One other possibility. I think there is a way to host your project on | googlecode but still have it mirrored on R-forge so from your users' | viewpoint its the same as if it were on R-Forge but you can use the | simpler googlecode site. In that case you might not need to set up | commits on R-Forge since you would do all your commits through | googlecode (depending on how it works) but I have not seen good | documentation on how to do this. | | | | __ | R-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- Registration is open for the 2nd International conference R / Finance 2010 See http://www.RinFinance.com for details, and see you in Chicago in April! __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
2010/3/27 Christophe Genolini cgeno...@u-paris10.fr: Henrik Bengtsson a écrit : 2010/3/27 hb h...@stat.berkeley.edu: On Sat, Mar 27, 2010 at 3:12 PM, Christophe Genolini cgeno...@u-paris10.fr wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. All looks ok, but I think you are using the wrong protocol. It should be 'svn+ssh' for *commits*, i.e. svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d which *is* shown at http://r-forge.r-project.org/scm/?group_id=727 Now, in addition, I configure putty as Uwe advice me. I follow the tutorial http://www.mono-project.com/Putty_and_TortoiseSvn Sorry, I missed that you've tried that (I scrolled past it on my small screen). - When you generated a key in PUTTYgen, did you enter a passphrase? I think you have to leave that blank. - Make sure not to have any newlines/spaces in the key, when you paste it, that is, you should have: Line 1: ssh-rsa Line 2: long key On two line ? On R-forge, they say /Make sure there are no line breaks except between keys./ My bad/you're right. I went back an checked an it's all on one line; I've got three keys on three lines. You can have multiple entries as the above. - You need to checkout with the svn+ssh URL, because that it is what TortoiseSVN will use for commits (unless you do relocate). If you can checkout using this protocol, you should be able to commit. Thus, focus your troubleshooting on checking out. - In the Default Settings PuTTY Configurations, make sure Attempt authentication using Pageant is checked under the Connection - SSH - Auth panel. I did - Make sure Pageant lists the key in its dialog. It is. Does it work? No. In putty, I get : login as: christophe Then a pop up say : Assertion failed! Program:...\pageant.exe File: ..\sshrsa.c Line:793 ... Hmm... I don't get that. It looks wrong. Google it and you find: quote 10.7 ‘Internal error’, ‘Internal fault’, ‘Assertion failed’ Any error beginning with the word ‘Internal’ should never occur. If it does, there is a bug in PuTTY by definition; please see appendix B and report it to us. Similarly, any error message starting with ‘Assertion failed’ is a bug in PuTTY. Please report it to us, and include the exact text from the error message box. /quote URL: http://the.earth.li/~sgtatham/putty/0.60/htmldoc/Chapter10.html#errors-internal Also: http://www.chiark.greenend.org.uk/~sgtatham/putty/wishlist/sshcrcda-assertion-failed.html What's the PuTTY version do you have? I have PuTTY v0.60 and it works. Try to generate a new pair of ssh keys and retry. If you want to, you can send me a pair of private/public keys that you generate and I can try it on my r-forge account. /Henrik Then I click ignore On putty again : Authenticating with public key rsa-key-20100327 from agent Access denied christo...@kml3d.r-forge.r-project.org's password: Linux xmrforge2 2.6.18-xen #1 SMP Fri May 18 16:01:42 BST 2007 x86_64 The programs included with the Debian GNU/Linux system are free software; the exact distribution terms for each program are described in the individual files in /usr/share/doc/*/copyright. Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent permitted by applicable law. Last login: Sat Mar 27 17:56:55 2010 from def92-4-82-225-59-146.fbx.proxad.net This is a restricted account. You cannot execute anything here. Goodbye. /Henrik /Henrik PS. Don't think you need plink, but I might be wrong. I also see on some tutorial that we might need putty.exe or plink.exe. I download them, but R-Forge user Manual do not mention them. Any idea of what goes wrong ? Thanks Christophe __ R-devel@r
Re: [Rd] Using SVN + SSH on windows
I wasn't commenting of the overall worth of the system or the efforts of those involved in it but your experience is with Linux rather than Windows and I don't think you understand the problems that Windows users have with this. The poster may have believed its uniquely his problem but in fact others have had very similar problems in dealing with this. What is the purpose of this list if its not to share experiences to help one another? I think the useful suggestions I made could potentially save someone literally days of frustration and my other suggestions could possibly overcome these problems in part making the system more useful so I don't agree that this is mere complaining. On Sat, Mar 27, 2010 at 2:15 PM, Dirk Eddelbuettel e...@debian.org wrote: On 27 March 2010 at 13:50, Gabor Grothendieck wrote: | The worst part is the 20 minute delay which means that if here is | something wrong and you don't know what it is and need to try various | things via trial and error each try takes 20 minutes so its not | surprising that it can be extremely time consuming to set up. I did | set it up a long time ago so perhaps the situation is better now but | my experience at the time was more like Christophe's. If the 20 | minute turnaround cannot be solved then I think the best solution for | Windows users would be excellent step by step documentation on how to | mirror your repository onto R-Forge from googlecode and elsewhere so | that Windows users can do their commits on googlecode (assuming that | mirroring your repository is possible and is easier than the commit | procedure and does not involve the 20 minute delay). I think you are being rather unfair here. These are contributed service being provided by folks in their extra time that they could be spending for their own work or research instead. The general rule still is: stop complaining, and volunteer to provide something that is better (or at least write the aforementioned step-by-step tutorial). Otherwise you are just making noise with no signal whatsoever. R-Forge is a rocksolid service for hundreds of us, and (at least the folks I work with) are very appreciative of the service. So a big Thank You from my end. Dirk | 2010/3/27 Uwe Ligges lig...@statistik.tu-dortmund.de: | It is really not hard to set it up. I am using a vanilla ssh (rather than | putty) and that works fine all the time... | | Uwe Ligges | | | On 27.03.2010 18:31, Gabor Grothendieck wrote: | | s getting commits to R-Forge to work from | Windows. The entire system is really geared to UNIX. It took me a | couple of days of trial and error (since you have to wait 20 minutes | for each try) before I got it working. Although I did get it to work, | I ultimately decided to host all my packages on googlecode. | googlecode is extremely easy to use from Windows and does not require | any public/private key, pageant, etc. e.g. | http://sqldf.googlecode.com. If you already have TortoiseSVN and know | how to use it then you can probably set up a googlecode site in | literally 5 minutes. | | One other possibility. I think there is a way to host your project on | googlecode but still have it mirrored on R-forge so from your users' | viewpoint its the same as if it were on R-Forge but you can use the | simpler googlecode site. In that case you might not need to set up | commits on R-Forge since you would do all your commits through | googlecode (depending on how it works) but I have not seen good | documentation on how to do this. | | | | __ | R-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- Registration is open for the 2nd International conference R / Finance 2010 See http://www.RinFinance.com for details, and see you in Chicago in April! __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
BTW, it may indeed be that you have to wait (more than 2-3 hours) before things are updated on the r-forge servers, cf. Thread 'FYI: New members must wait hours to commit' on 2009-12-03 https://r-forge.r-project.org/forum/forum.php?thread_id=1966forum_id=78 /Henrik On Sat, Mar 27, 2010 at 7:30 PM, Henrik Bengtsson h...@stat.berkeley.edu wrote: 2010/3/27 Christophe Genolini cgeno...@u-paris10.fr: Henrik Bengtsson a écrit : 2010/3/27 hb h...@stat.berkeley.edu: On Sat, Mar 27, 2010 at 3:12 PM, Christophe Genolini cgeno...@u-paris10.fr wrote: Hi the list, I try to use R-Forge for developping a projet. I am using tortoise SVN (last version) but I do not manage to Commit. I read the R-Forge user Manual and some post on but I do not manage to find the solution. Here is what I did: 1/ I download 'puttygen.exe'. I generate a key (256 bits). 2/ I save the private key in a file 'private.ppk' on my computer. 3/ I copy-paste the public key on sourceforge ssh-rsa B3NzaC1yc2EBJQAAACEAobwycGGZrMZ39i7Vtrdk3ahN1hVw/tPoiShJGk1xjRs= rsa-key-20100327 4/ I wait two hours. 5/ On my computer, I run 'pageant.exe'. 6/ I click on 'Add key'. I load the file 'private.ppk' 7/ I close 'pageant.exe' (still actif in the task bar). 8/ I open explorer. I create a directory that is suppose to be the local directoy for the projet. 9/ I right-click on the directory. I open 'SVN checkout' 10/ In 'URL of repository:', I write : 'svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d' (christophe is my accoung, kml3d is the project) And... ...nothing happen. No bug, not warning, nothing. I try several things: if I do 'svn://christo...@svn.r-forge.r-project.org/svnroot/kml3d', I do manage to download the project. But then, I do not manage to upload some modification. All looks ok, but I think you are using the wrong protocol. It should be 'svn+ssh' for *commits*, i.e. svn+ssh://christo...@svn.r-forge.r-project.org/svnroot/kml3d which *is* shown at http://r-forge.r-project.org/scm/?group_id=727 Now, in addition, I configure putty as Uwe advice me. I follow the tutorial http://www.mono-project.com/Putty_and_TortoiseSvn Sorry, I missed that you've tried that (I scrolled past it on my small screen). - When you generated a key in PUTTYgen, did you enter a passphrase? I think you have to leave that blank. - Make sure not to have any newlines/spaces in the key, when you paste it, that is, you should have: Line 1: ssh-rsa Line 2: long key On two line ? On R-forge, they say /Make sure there are no line breaks except between keys./ My bad/you're right. I went back an checked an it's all on one line; I've got three keys on three lines. You can have multiple entries as the above. - You need to checkout with the svn+ssh URL, because that it is what TortoiseSVN will use for commits (unless you do relocate). If you can checkout using this protocol, you should be able to commit. Thus, focus your troubleshooting on checking out. - In the Default Settings PuTTY Configurations, make sure Attempt authentication using Pageant is checked under the Connection - SSH - Auth panel. I did - Make sure Pageant lists the key in its dialog. It is. Does it work? No. In putty, I get : login as: christophe Then a pop up say : Assertion failed! Program:...\pageant.exe File: ..\sshrsa.c Line:793 ... Hmm... I don't get that. It looks wrong. Google it and you find: quote 10.7 ‘Internal error’, ‘Internal fault’, ‘Assertion failed’ Any error beginning with the word ‘Internal’ should never occur. If it does, there is a bug in PuTTY by definition; please see appendix B and report it to us. Similarly, any error message starting with ‘Assertion failed’ is a bug in PuTTY. Please report it to us, and include the exact text from the error message box. /quote URL: http://the.earth.li/~sgtatham/putty/0.60/htmldoc/Chapter10.html#errors-internal Also: http://www.chiark.greenend.org.uk/~sgtatham/putty/wishlist/sshcrcda-assertion-failed.html What's the PuTTY version do you have? I have PuTTY v0.60 and it works. Try to generate a new pair of ssh keys and retry. If you want to, you can send me a pair of private/public keys that you generate and I can try it on my r-forge account. /Henrik Then I click ignore On putty again : Authenticating with public key rsa-key-20100327 from agent Access denied christo...@kml3d.r-forge.r-project.org's password: Linux xmrforge2 2.6.18-xen #1 SMP Fri May 18 16:01:42 BST 2007 x86_64 The programs included with the Debian GNU/Linux system are free software; the exact distribution terms for each program are described in the individual files in /usr/share/doc/*/copyright. Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent permitted by applicable law. Last login: Sat Mar 27 17:56:55 2010 from def92-4-82-225-59-146.fbx.proxad.net This is a restricted account. You
Re: [Rd] update.packages(1)
On 25/03/2010 3:16 PM, Arni Magnusson wrote: I'm relaying a question from my institute's sysadmin: Would it be possible to modify update.packages() and related functions so that 'lib.loc' accepts integer values to specify a library from the .libPaths() vector? Many Linux users want to update all user packages (inside the R_LIBS_USER directory, e.g. ~/r/library) and none of the system packages (inside the /usr directory, e.g. /usr/lib64/R/library), because they don't have write privileges to update the system packages. Currently, this can be done by pressing 'y RET' for all the user packages and 'RET' for all the system packages. This hard work and careful reading when there dozens of packages. Another way is to run update.packages(Sys.getenv(R_LIBS_USER)) or: update.packages(.libPaths()[1]) You could also save some work by putting ask=FALSE, or ask=graphics in as another argument. But isn't it easy enough to write your own function as a wrapper to update.packages, suiting your own local conventions? It seems like a bad idea to make update.packages too friendly, when there are several different friendly front-ends for it already (e.g. the menu entries in Windows or MacOS GUIs). But it would be nicer for the user to type update.packages(1) using a 'pos' like notation to indicate the first element of the .libPaths() vector. --- A separate but related issue is that it would be nice if the R_LIBS_USER library would be the first library by default. Currently, my sysadmin must use Rprofile.site to shuffle the .libPaths() to make R_LIBS_USER first, which seems like a sensible default when it comes to install.packages() and remove.packages(). This is R version 2.10.1 (2009-12-14) on x86_64-redhat-linux-gnu (Fedora 11). I didn't write it, but I suspect the current behaviour was intentional. Without it, it would be hard to put the user library last, since .libPaths() adds things at the front. Now you have a choice: use the R_LIBS_USER environment variable to put it last, use a line in your Rprofile.site file to put something first. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages(1)
On 3/27/10 1:43 PM, Duncan Murdoch wrote: On 25/03/2010 3:16 PM, Arni Magnusson wrote: I'm relaying a question from my institute's sysadmin: Would it be possible to modify update.packages() and related functions so that 'lib.loc' accepts integer values to specify a library from the .libPaths() vector? Many Linux users want to update all user packages (inside the R_LIBS_USER directory, e.g. ~/r/library) and none of the system packages (inside the /usr directory, e.g. /usr/lib64/R/library), because they don't have write privileges to update the system packages. Currently, this can be done by pressing 'y RET' for all the user packages and 'RET' for all the system packages. This hard work and careful reading when there dozens of packages. Another way is to run update.packages(Sys.getenv(R_LIBS_USER)) or: update.packages(.libPaths()[1]) You could also save some work by putting ask=FALSE, or ask=graphics in as another argument. But isn't it easy enough to write your own function as a wrapper to update.packages, suiting your own local conventions? It seems like a bad idea to make update.packages too friendly, when there are several different friendly front-ends for it already (e.g. the menu entries in Windows or MacOS GUIs). But it would be nicer for the user to type update.packages(1) using a 'pos' like notation to indicate the first element of the .libPaths() vector. --- A separate but related issue is that it would be nice if the R_LIBS_USER library would be the first library by default. Currently, my sysadmin must use Rprofile.site to shuffle the .libPaths() to make R_LIBS_USER first, which seems like a sensible default when it comes to install.packages() and remove.packages(). I'm confused. AFAICT, R_LIBS_USER _is_ put first. Following the advice in the Admin manual, I created a directory matching the default value of R_LIBS_USER (Sys.getenv(R_LIBS_USER) to see it). Then when I start R, I get: .libPaths() [1] /home/sfalcon/R/x86_64-unknown-linux-gnu-library/2.11 [2] /home/sfalcon/build/rd/library Isn't that what you want? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages(1)
On 27/03/2010 4:48 PM, Seth Falcon wrote: On 3/27/10 1:43 PM, Duncan Murdoch wrote: On 25/03/2010 3:16 PM, Arni Magnusson wrote: I'm relaying a question from my institute's sysadmin: Would it be possible to modify update.packages() and related functions so that 'lib.loc' accepts integer values to specify a library from the .libPaths() vector? Many Linux users want to update all user packages (inside the R_LIBS_USER directory, e.g. ~/r/library) and none of the system packages (inside the /usr directory, e.g. /usr/lib64/R/library), because they don't have write privileges to update the system packages. Currently, this can be done by pressing 'y RET' for all the user packages and 'RET' for all the system packages. This hard work and careful reading when there dozens of packages. Another way is to run update.packages(Sys.getenv(R_LIBS_USER)) or: update.packages(.libPaths()[1]) You could also save some work by putting ask=FALSE, or ask=graphics in as another argument. But isn't it easy enough to write your own function as a wrapper to update.packages, suiting your own local conventions? It seems like a bad idea to make update.packages too friendly, when there are several different friendly front-ends for it already (e.g. the menu entries in Windows or MacOS GUIs). But it would be nicer for the user to type update.packages(1) using a 'pos' like notation to indicate the first element of the .libPaths() vector. --- A separate but related issue is that it would be nice if the R_LIBS_USER library would be the first library by default. Currently, my sysadmin must use Rprofile.site to shuffle the .libPaths() to make R_LIBS_USER first, which seems like a sensible default when it comes to install.packages() and remove.packages(). I'm confused. AFAICT, R_LIBS_USER _is_ put first. Following the advice in the Admin manual, I created a directory matching the default value of R_LIBS_USER (Sys.getenv(R_LIBS_USER) to see it). Then when I start R, I get: .libPaths() [1] /home/sfalcon/R/x86_64-unknown-linux-gnu-library/2.11 [2] /home/sfalcon/build/rd/library Isn't that what you want? I didn't try it, I just read the documentation (in ?.libPaths). As I read it it says the order is R_LIBS, R_LIBS_USER, .Library.site, .Library and some of those components can be missing. So another way to put the user libs first is to specify the site libs in .Library.site rather than in the environment variable. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Using SVN + SSH on windows
Uwe Ligges wrote: It is really not hard to set it up. I am using a vanilla ssh (rather than putty) and that works fine all the time... Uwe Ligges Ditto here. I am using ssh non commercial version with tortoise on Vista, and I don't recall any problems setting it up. R-forge works perfectly fine with windows and tortoise in my experience. Is your putty/ssh working? Can you access other machines with it? I do recall ssh can be a bit fussy. David Scott On 27.03.2010 18:31, Gabor Grothendieck wrote: s getting commits to R-Forge to work from Windows. The entire system is really geared to UNIX. It took me a couple of days of trial and error (since you have to wait 20 minutes for each try) before I got it working. Although I did get it to work, I ultimately decided to host all my packages on googlecode. googlecode is extremely easy to use from Windows and does not require any public/private key, pageant, etc. e.g. http://sqldf.googlecode.com. If you already have TortoiseSVN and know how to use it then you can probably set up a googlecode site in literally 5 minutes. One other possibility. I think there is a way to host your project on googlecode but still have it mirrored on R-forge so from your users' viewpoint its the same as if it were on R-Forge but you can use the simpler googlecode site. In that case you might not need to set up commits on R-Forge since you would do all your commits through googlecode (depending on how it works) but I have not seen good documentation on how to do this. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- _ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] : Operator overloading for custom classes
Thank you for replying! But I have since figured out how to perform the
operator overloading after reading the Not so short tutorial to S4 classes
and a bit of Robert Gentleman's deceptively titled book on R.
(I had mistakenly posted to r-devel earlier and when I posted to r-help
subsequently I got a pointer to the resources on rwiki that dealt with OOP)
Like you say, many already existing packages inside of R use operator
overloading. For instance I later observed that the + operator was
overloaded [by running the command methods('+')] for the Date and POSIXt
classes. I will have to redefine the generic function + for my classes to
get the output I want.
Regards,
Chillu
On Sat, Mar 27, 2010 at 3:46 AM, Peter Ruckdeschel peter.ruckdesc...@web.de
wrote:
I need some help to get some of the object orientation, specifically the
methods that overload the basic arithmetic operations, from sample C++
code to R. I don't have experience with such advanced language features
inside of R. So I was wondering if some of you could help me out in this
regard.
I have written a simple demonstration of a forward mode automatic
differentiator in C++ and it is currently hosted on github:
http://github.com/quantumelixir/ad-demo/blob/master/simple.cpp. It uses
simple operator overloading techniques to modify the meaning of the
basic arithmetic operations (+, -, *, /) for the derivative type Dual
number class that I have defined. Could you show me how this could be
equivalently done in R? I want to know how to define custom classes and
define the meaning of arithmetic for them.
I had checked for operator overloading in R but could only find the
equivalence of a + b and '+'(a, b) in the R language definition. Could
you show how I could extend the simple object oriented-ness in the C++
code neatly to R?
Thanks a bunch!
Chillu
[[alternative HTML version deleted]]
First of all you should read about S4 classes, in particular
the books of John Chambers should be helpful ;-)
(others on this list might point you to further sources).
The key is to define S4 classes for your operands
[i.e; if I have understood correctly you would implement
your Dual number class as S4 class].
Then you would define new methods by setMethod().
Not sure whether this gives you the indications you look for,
but we have overloaded arithmetic operators to act on distribution
classes in package distr (cf CRAN, developped under r-forge).
You might want to look at the code in NormalDistribution.R resp.
ContDistribution.R
HTH Peter Ruckdeschel
__
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[[alternative HTML version deleted]]
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Re: [Rd] Suggestion: Not having to export .conflicts.OK in name spaces
Hi.
On Mon, Mar 22, 2010 at 5:36 PM, Seth Falcon s...@userprimary.net wrote:
On 3/22/10 3:57 AM, Martin Maechler wrote:
SF == Seth Falcons...@userprimary.net
on Fri, 19 Mar 2010 13:47:17 -0700 writes:
SF On 3/17/10 9:11 AM, Henrik Bengtsson wrote:
Currently library() and attach() fail to locate an
existing '.conflicts.OK' in a package wit name space,
unless it is exported. Since there should be little
interest in exporting '.conflicts.OK' otherwise, one may
argue that those methods should look for '.conflicts.OK'
even if it is not exported.
SF I guess I agree that there is no real value in forcing
SF .conflicts.OK to be exported.
so do I.
So I guess we agree that Henrik's patch would be worth applying.
@Henrik: if you resend your patch with the additions for attach, I will see
about putting it in.
When looking more carefully at base::attach(), I see that there is
nothing to do, because attach() takes a data.frame, a list, an
environment, NULL, or a file saved using base::save(). None of these
can have a name space.
The scenario I was worrying about was when you attach() the
environment of a package with a namespace, e.g.
envir - as.environment(package:graphics);
envir2 - attach(envir, name=foo);
ls(envir=envir2, all.names=TRUE);
but to the best of my understanding it is only exported objects that
are attached, i.e. if .conflicts.OK is not exported by the package,
then it won't be attached and hence not exist either way. Is that
correct?
envir - as.environment(package:R.utils);
envir2 - attach(envir, name=foo);
ls(envir=envir2, all.names=TRUE);
SF OTOH, this seems like a dubious feature to begin. When
SF is it a good idea to use it?
in cases, the package author thinks (s)he knows what (s)he is
doing;
e.g. in the case of Matrix, I could argue that I know about the
current conflicts, and I would *not* want the users of my
package be intimidated by warnings about maskings...
I can't say that this convinces me that .conflicts.OK is OK. Are there
package authors who realize they do not know what they are doing enough to
keep the warning messages :-P
I define throw.default() in R.methodsS3:
R.methodsS3::throw.default
function (...)
{
stop(...)
}
environment: namespace:R.methodsS3
In R.oo, which loads R.methodsS3, I override this with:
R.oo::throw.default
function (...)
{
throw(Exception(...))
}
environment: namespace:R.oo
The Exception class is defined in R.oo. If someone loads R.methodsS3
alone, you get a throw() method. Someone loading R.oo will get the a
throw() that is backward compatible but with some extra bells and
whistles recording the strack trace etc. This is an intended design.
So when I load R.oo, I don't want the warning of overloading throw()
in R.methodsS3. Is there an alternative for me?
Ideally, there should be a way to specify which objects are ok,
instead of all or none.
Thanks
Henrik
+ seth
--
Seth Falcon | @sfalcon | http://userprimary.net/
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