[sage-support] I need a bit of git handholding...
Dear list I noted problems with freetype on my machine ; Volker Braun diagnosed (in this thread https://groups.google.com/forum/#!topic/sage-support/FnTEcpfg6wE) that the current sage's freetype had problems with fonts currently installed on my machine. Therefore I went ahead, created trac#15561http://trac.sagemath.org/ticket/15561 and, on my current tree, created the branch, installed the current upstream tarball, upated the relevant foles a,d created a small patch for libpng. On my machine, the results were OK, so I pushed the resulting branch to the track ticket. But I have two problems with this branch : 1) working on another machine, with a brand-new sage tree, I have not been able to get my work back : sage -dev checkout --ticket 15561 sage -dev diff gives me an empty diff. 2) As displayed by trac, the btranch does not contain any mention of the new source tarball... If a kind soul could point me to the direction(s) and module(s) of my error(s), I'd be grateful. -- Emmanuel Charpentier -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
The tarball is *not* part of the git repository, only its checksum. You need to indicate on the ticket if you need any additional tarball, which (at least for now) will the be copied manually to http://www.sagemath.org/packages/upstream/ On Sunday, December 22, 2013 9:32:57 AM UTC, Emmanuel Charpentier wrote: Dear list I noted problems with freetype on my machine ; Volker Braun diagnosed (in this thread https://groups.google.com/forum/#!topic/sage-support/FnTEcpfg6wE) that the current sage's freetype had problems with fonts currently installed on my machine. Therefore I went ahead, created trac#15561http://trac.sagemath.org/ticket/15561 and, on my current tree, created the branch, installed the current upstream tarball, upated the relevant foles a,d created a small patch for libpng. On my machine, the results were OK, so I pushed the resulting branch to the track ticket. But I have two problems with this branch : 1) working on another machine, with a brand-new sage tree, I have not been able to get my work back : sage -dev checkout --ticket 15561 sage -dev diff gives me an empty diff. 2) As displayed by trac, the btranch does not contain any mention of the new source tarball... If a kind soul could point me to the direction(s) and module(s) of my error(s), I'd be grateful. -- Emmanuel Charpentier -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: Failed compile of Sage 5.13, ATLAS spkg on PowerBook G4, OS X 10.5.8
Whats the content of your /usr/local/sage-5.13/spkg/build/atlas-3.10.1.p7/src/ATLAS-build/lib/ directory, there should be a liblapack but apparently is not. Maybe search through the whole log to see if there were any errors with lapack On Sunday, December 22, 2013 5:37:41 AM UTC, Alexander Power wrote: *export SAGE_ATLAS_ARCH=PPCG4,AltiVec* This'll force compilation of ATLAS instead of using Apple's own libraries, for the record. -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
Dear Volker, Thank you for this note. I added a relevant comment to the tickethttp://trac.sagemath.org/ticket/15561 (and attached the tarball, since it's a small one). Any idea about how to retrieve this branch on another machine (with the same trac identifier, of course...) ? -- Emmanuel Charpentier Le dimanche 22 décembre 2013 12:24:28 UTC+1, Volker Braun a écrit : The tarball is *not* part of the git repository, only its checksum. You need to indicate on the ticket if you need any additional tarball, which (at least for now) will the be copied manually to http://www.sagemath.org/packages/upstream/ On Sunday, December 22, 2013 9:32:57 AM UTC, Emmanuel Charpentier wrote: Dear list I noted problems with freetype on my machine ; Volker Braun diagnosed (in this thread https://groups.google.com/forum/#!topic/sage-support/FnTEcpfg6wE) that the current sage's freetype had problems with fonts currently installed on my machine. Therefore I went ahead, created trac#15561http://trac.sagemath.org/ticket/15561 and, on my current tree, created the branch, installed the current upstream tarball, upated the relevant foles a,d created a small patch for libpng. On my machine, the results were OK, so I pushed the resulting branch to the track ticket. But I have two problems with this branch : 1) working on another machine, with a brand-new sage tree, I have not been able to get my work back : sage -dev checkout --ticket 15561 sage -dev diff gives me an empty diff. 2) As displayed by trac, the btranch does not contain any mention of the new source tarball... If a kind soul could point me to the direction(s) and module(s) of my error(s), I'd be grateful. -- Emmanuel Charpentier -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
On Sunday, December 22, 2013 9:32:57 AM UTC, Emmanuel Charpentier wrote: 1) working on another machine, with a brand-new sage tree, I have not been able to get my work back : sage -dev checkout --ticket 15561 This does work. See the output of git log: $ git log -4 commit f570a62601eea75502fa2bab4431643fa1cbc2c7 Author: Emmanuel Charpentier emm.charpent...@free.fr Date: Sat Dec 21 14:53:58 2013 +0100 Fixed patching of libpng. commit de6e2ee221e49e7ccbcabf731e284b91df9bb919 Author: Emmanuel Charpentier emm.charpent...@free.fr Date: Sat Dec 21 14:30:32 2013 +0100 Patching libpng to allow compilation of libfreetype-2.5.2 commit 5a4c66b9f9a45ea44e3ac9270311d6f68c05f1ae Author: Emmanuel Charpentier emm.charpent...@free.fr Date: Sat Dec 21 09:39:35 2013 +0100 Upgrading to current upstream stable release Also added license information to the SPKG.txt file. commit 3472a854df051b57d1cb7e4934913f17f1fef820 Author: Volker Braun vbraun.n...@gmail.com Date: Tue Dec 17 18:08:15 2013 + Updated Sage version to 6.0 sage -dev diff gives me an empty diff. It shows you the diff relative to the current directory. If you were to make any (uncommitted) changes, then they would show up here. If you want to see the diff relative to an older version (say, the master branch), you'd have to do sage -dev diff --base master Or directly with git: git diff master..HEAD# HEAD=current branch head git diff master.. # abbreviated version -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
The dev object in Sage is equivalent to the sage -dev command line. Arguments are translated between Python to Shell calling conventions, so $ sage -dev diff --base master is the same as sage: dev.diff(base='master') Help overview: $ sage -dev help usage: sage-dev [-h] subcommand ... The developer interface for sage. optional arguments: -h, --helpshow this help message and exit subcommands: abandon Abandon a ticket or branch. checkoutCheckout another branch. clean Restore the working directory to the most recent commit. comment Add a comment to ticket on trac. commit Create a commit from the pending changes on the current branch. create-ticket Create a new ticket on trac. diffShow how the current file system differs from base. download-patch Legacy support: Download a patch to a temporary directory. edit-ticket Edit the description of ticket on trac. helpshow help message and exit import-patchLegacy support: Import a patch into the current branch. merge Merge changes from ticket_or_branch into the current branch. needs-info Set a ticket on trac to needs_info. needs-reviewSet a ticket on trac to needs_review. needs-work Set a ticket on trac to needs_work. positive-review Set a ticket on trac to positive_review. prune-tickets Remove branches for tickets that are already merged into master. pullPull ticket_or_remote_branch to branch. pushPush the current branch to the Sage repository. remote-status Show information about the status of ticket. set-remote Set the remote branch to push to for branch_or_ticket to remote_branch. show-dependencies Show the dependencies of ticket. tickets Print the tickets currently being worked on in your local repository. upload-ssh-key Upload public_key to gitolite through the trac interface. vanilla Return to a clean version of Sage. Help for subcommands: $ sage -dev diff -husage: sage-dev diff [-h] [--base BASE] Show how the current file system differs from base. optional arguments: -h, --help show this help message and exit --base BASE a string; show the differences against the latest 'commit' (the default), against the branch 'master' (or any other branch name), or the merge of the 'dependencies' of the current ticket (if the dependencies merge cleanly) On Sunday, December 22, 2013 3:22:42 PM UTC, Emmanuel Charpentier wrote: Thank you very much, Volker ! I definitely need to take some time to **learn** git. BTW : the -dev commands currently have no direct documentation *per se*. There is a lot of examples in the developer's guide, and the reference manual has a SageDev section, but neither is clear as to what sage functions have a script counterpart, or the possible differences between sage functions and scripts. -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
Thanks to Volker's explanations, the relevant tickethttp://trac.sagemath.org/ticket/15561 is again at needs review. Thanks a lot for your help. -- Emmanuel Charpentier Le dimanche 22 décembre 2013 16:22:42 UTC+1, Emmanuel Charpentier a écrit : Thank you very much, Volker ! I definitely need to take some time to **learn** git. BTW : the -dev commands currently have no direct documentation *per se*. There is a lot of examples in the developer's guide, and the reference manual has a SageDev section, but neither is clear as to what sage functions have a script counterpart, or the possible differences between sage functions and scripts. Le dimanche 22 décembre 2013 14:49:27 UTC+1, Volker Braun a écrit : On Sunday, December 22, 2013 9:32:57 AM UTC, Emmanuel Charpentier wrote: 1) working on another machine, with a brand-new sage tree, I have not been able to get my work back : sage -dev checkout --ticket 15561 This does work. See the output of git log: $ git log -4 commit f570a62601eea75502fa2bab4431643fa1cbc2c7 Author: Emmanuel Charpentier emm.cha...@free.fr Date: Sat Dec 21 14:53:58 2013 +0100 Fixed patching of libpng. commit de6e2ee221e49e7ccbcabf731e284b91df9bb919 Author: Emmanuel Charpentier emm.cha...@free.fr Date: Sat Dec 21 14:30:32 2013 +0100 Patching libpng to allow compilation of libfreetype-2.5.2 commit 5a4c66b9f9a45ea44e3ac9270311d6f68c05f1ae Author: Emmanuel Charpentier emm.cha...@free.fr Date: Sat Dec 21 09:39:35 2013 +0100 Upgrading to current upstream stable release Also added license information to the SPKG.txt file. commit 3472a854df051b57d1cb7e4934913f17f1fef820 Author: Volker Braun vbrau...@gmail.com Date: Tue Dec 17 18:08:15 2013 + Updated Sage version to 6.0 sage -dev diff gives me an empty diff. It shows you the diff relative to the current directory. If you were to make any (uncommitted) changes, then they would show up here. If you want to see the diff relative to an older version (say, the master branch), you'd have to do sage -dev diff --base master Or directly with git: git diff master..HEAD# HEAD=current branch head git diff master.. # abbreviated version -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Re: I need a bit of git handholding...
Thank you. I missed that online help. Silly me... -- Emmanuel Charpentier Le dimanche 22 décembre 2013 16:39:27 UTC+1, Volker Braun a écrit : The dev object in Sage is equivalent to the sage -dev command line. Arguments are translated between Python to Shell calling conventions, so $ sage -dev diff --base master is the same as sage: dev.diff(base='master') Help overview: $ sage -dev help usage: sage-dev [-h] subcommand ... The developer interface for sage. optional arguments: -h, --helpshow this help message and exit subcommands: abandon Abandon a ticket or branch. checkoutCheckout another branch. clean Restore the working directory to the most recent commit. comment Add a comment to ticket on trac. commit Create a commit from the pending changes on the current branch. create-ticket Create a new ticket on trac. diffShow how the current file system differs from base. download-patch Legacy support: Download a patch to a temporary directory. edit-ticket Edit the description of ticket on trac. helpshow help message and exit import-patchLegacy support: Import a patch into the current branch. merge Merge changes from ticket_or_branch into the current branch. needs-info Set a ticket on trac to needs_info. needs-reviewSet a ticket on trac to needs_review. needs-work Set a ticket on trac to needs_work. positive-review Set a ticket on trac to positive_review. prune-tickets Remove branches for tickets that are already merged into master. pullPull ticket_or_remote_branch to branch. pushPush the current branch to the Sage repository. remote-status Show information about the status of ticket. set-remote Set the remote branch to push to for branch_or_ticket to remote_branch. show-dependencies Show the dependencies of ticket. tickets Print the tickets currently being worked on in your local repository. upload-ssh-key Upload public_key to gitolite through the trac interface. vanilla Return to a clean version of Sage. Help for subcommands: $ sage -dev diff -husage: sage-dev diff [-h] [--base BASE] Show how the current file system differs from base. optional arguments: -h, --help show this help message and exit --base BASE a string; show the differences against the latest 'commit' (the default), against the branch 'master' (or any other branch name), or the merge of the 'dependencies' of the current ticket (if the dependencies merge cleanly) On Sunday, December 22, 2013 3:22:42 PM UTC, Emmanuel Charpentier wrote: Thank you very much, Volker ! I definitely need to take some time to **learn** git. BTW : the -dev commands currently have no direct documentation *per se*. There is a lot of examples in the developer's guide, and the reference manual has a SageDev section, but neither is clear as to what sage functions have a script counterpart, or the possible differences between sage functions and scripts. -- You received this message because you are subscribed to the Google Groups sage-support group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at http://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/groups/opt_out.
[sage-support] Sage's R (6.0) mucks up path and libraries search on amd64 (at least Debian).
Sage's 6.0 implementation seems to muck up the way R finds libraries and/or executables on amd64, at least on Debian systems. My main system is Debian (testing) running on a Core i7 laptop with plenty of RAM. I've also set up a virtual machine (VirtualBox) with i686 Debian in order to cross-compile for a small subnotebook (where a real compilation takes in excess of 24 hours). I've had problems with the latest Sage (6.0) release. A first one, related to system fonts unsupported by Sage's freetype, has been reported elsewhere, ticketed, and a port of freetype 2.5.2 proposed (hint : trac#15561 http://trac.sagemath.org/ticket/15561 needs review). I've encountered this problem on both amd64 and i686 machines, but not on a smaller amd64 machine, with a tad older system software. I encountered a second problem on amd64 machines only, hence the present post. In short, some R packages using external libraries cannot be installed anymore. Furthermore, tcl/tk is no longer available to Sage's R. This on machines where system's R (Debian packages in all cases) has no problem whatsoever. First case in point : tcl/tk. From R's compilation log : [ ... ] checking for tclConfig.sh... no checking for tclConfig.sh in library (sub)directories... no checking for tkConfig.sh... no checking for tkConfig.sh in library (sub)directories... no checking for tcl.h... no [ ... ] However : charpent@asus16-ec:~$ locate tclConfig.sh /home/charpent/Dev/tcltk/tcl8.6.1/pkgs/itcl4.0.0/itclConfig.sh.in /home/charpent/Dev/tcltk/tcl8.6.1/unix/tclConfig.sh /home/charpent/Dev/tcltk/tcl8.6.1/unix/tclConfig.sh.in /home/charpent/Dev/tcltk/tcl8.6.1/win/tclConfig.sh.in /usr/lib/tclConfig.sh /usr/lib/tcl8.5/tclConfig.sh charpent@asus16-ec:~$ locate tkConfig.sh /home/charpent/Dev/tcltk/tk8.6.1/unix/tkConfig.sh.in /home/charpent/Dev/tcltk/tk8.6.1/win/tkConfig.sh.in /usr/lib/tkConfig.sh /usr/lib/tk8.5/tkConfig.sh charpent@asus16-ec:~$ locate tcl.h /home/charpent/Dev/tcltk/tcl8.6.1/generic/tcl.h /home/charpent/Dev/tcltk/tcl8.6.1/pkgs/itcl4.0.0/generic/itcl.h /home/charpent/Dev/tcltk/tcl8.6.1/tools/tcl.hpj.in /home/charpent/Dev/tcltk/tcl8.6.1/win/tcl.hpj.in /usr/include/tcl8.5/tcl.h /usr/include/tcl8.5/tcl-private/generic/tcl.h /usr/share/doc/graphviz/examples/demo/entities.tcl.html /usr/share/doc/postgresql-doc-9.3/html/pltcl.html /usr/share/doc/texlive-doc/latex/koma-script/scrartcl.html As a consequence, tcltk is unavailable in Sage's R, which is not really important per se, but renders tkrplot (not really important), gsubfn (much more important) and sqldf (almost vital) R packages uninstallable. Second case : rjags install.packages(rjags) essai de l'URL 'http://cran.univ-paris1.fr/src/contrib/rjags_3-11.tar.gz' Content type 'application/x-gzip' length 65594 bytes (64 Kb) URL ouverte == downloaded 64 Kb * installing *source* package ‘rjags’ ... ** package ‘rjags’ correctement décompressé et sommes MD5 vérifiées checking for prefix by checking for jags... /usr/bin/jags checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking Console.h usability... yes checking Console.h presence... yes checking for Console.h... yes checking for gcc... gcc -std=gnu99 checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for jags_version in -ljags... yes configure: error: JAGS module directory /usr/lib64/JAGS/modules-3 does not exist. ERROR: configuration failed for package ‘rjags’ * removing ‘/home/charpent/sage/local/lib/R/library/rjags’ Les packages source téléchargés sont dans ‘/tmp/RtmpS0KOyC/downloaded_packages’ Message d'avis : In install.packages(rjags) : l'installation du package ‘rjags’ a eu un statut de sortie non nul Trying to install R2jags gives similar results for the same reason. This is **quite* serious* : JAGS is currently the only blackbox MCMC sampler able to sample from discrete distributions. Comparing with the system R installation of the same package hints at a possible cause : install.packages(rjags) Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) --- SVP sélectionner un miroir CRAN
