http://blog.gmane.org/gmane.linux.redhat.fedora.r.devel hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/299 <pre>Hi, In order to update some Bioconductor R libraries to their latest version I have a new dependency that has to be packaged. The review request is there: https://bugzilla.redhat.com/show_bug.cgi?id=821267 If someone has sometime to look into it :-) Thanks in advance! Pierre _______________________________________________ r-devel mailing list r-devel&lt; at &gt;lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2012-05-13T17:47:02 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/295 <pre>Hello, while chasing the several dependencies to build R-Sim-DiffProc I had to build R-rJava, at moment that is failing while testing the examples. Are there any suggestions to overcome this? * checking examples ... ERROR Running examples in 'rJava-Ex.R' failed The error most likely occurred in: [1] 0 + f &lt;- new(J("java.awt.Frame"), "Hello") + f$setVisible(TRUE) + } Error in .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", .jfindClass(class), : java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. Calls: new -&gt; new -&gt; .J -&gt; .jcall -&gt; .jcheck -&gt; .Call Execution halted error: Bad exit status from /tmp/rpmbuild/rpm-tmp.DdN0bT (%check) Regards, </pre> José Matos 2012-05-11T19:43:12 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/294 <pre>Hi, I have started to update a bunch of R packages to the latest version of bioconductor. Feel free to test and give karma: F17: https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc17,R-hgu95av2cdf-2.10.0-1.fc17,R-maanova-1.26.0-1.fc17,R-multtest-2.12.0-1.fc17,R-preprocessCore-1.18.0-1.fc17,R-ROC-1.32.0-1.fc17,R-qvalue-1.30.0-1.fc17,R-statmod-1.4.14-1.fc17,R-timeDate-2160.96-1.fc17,R-tkWidgets-1.34.0-1.fc17,R-DynDoc-1.34.0-1.fc17,R-widgetTools-1.34.0-1.fc17,R-XML-3.9.4-1.fc17,R-ALL-1.4.12-1.fc17,R-abind-1.4.0-2.fc17,R-BufferedMatrix-1.20.0-1.fc17 F16: https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc16,R-hgu95av2cdf-2.10.0-1.fc16,R-maanova-1.26.0-1.fc16,R-multtest-2.12.0-1.fc16,R-preprocessCore-1.18.0-1.fc16,R-ROC-1.32.0-1.fc16,R-qvalue-1.30.0-1.fc16,R-statmod-1.4.14-1.fc16,R-timeDate-2160.96-1.fc16,R-tkWidgets-1.34.0-1.fc16,R-DynDoc-1.34.0-1.fc16,R-widgetTools-1.34.0-1.fc16,R-XML-3.9.4-1.fc16,R-ALL-1.4.12-1.fc16,R-abind-1.4.0-1.fc16,R-BufferedMatrix-1.20.0-1.fc16 F15: https://admin</pre> Pierre-Yves Chibon 2012-04-26T15:07:06 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/291 <pre>Hi all, Although using the latest version of R from updates-testing: https://admin.fedoraproject.org/updates/FEDORA-2012-0119/ I could however recompile successfully R-zoo (arch specific) and R-widgetTools (noarch) from their latest git version without errors. I think this is worth noting. Good day, Pierre _______________________________________________ r-devel mailing list r-devel&lt; at &gt;lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2012-01-11T15:53:15 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/289 <pre>Dear all, To the great despair of spot, I have started to build CRAN and Bioconductor :-) This time, I am trying to make things cleaner and more accessible. I just uploaded all the spec files on github: https://github.com/pypingou/R-repo-spec and the scripts on: https://github.com/pypingou/R-repo-utility The whole project is hosted at http://r-repo.org At the moment everything is still in a early stage (for example, the r-repo-release rpm is not even done yet), but if you configure the repo by hand, you should be able to get RPMs. At least this time, if work becomes overwhelming again, what has been done will remain accessible :-) I would prefer to not announce this officially just yet, but some feedback be nice (thus this email). So if you feel like testing and are facing problem, let me know! Hope this helps, Best regards, Pierre _______________________________________________ r-devel mailing list r-devel&lt; at &gt;lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2012-01-04T08:43:25 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/289 <pre>Dear all, To the great despair of spot, I have started to build CRAN and Bioconductor :-) This time, I am trying to make things cleaner and more accessible. I just uploaded all the spec files on github: https://github.com/pypingou/R-repo-spec and the scripts on: https://github.com/pypingou/R-repo-utility The whole project is hosted at http://r-repo.org At the moment everything is still in a early stage (for example, the r-repo-release rpm is not even done yet), but if you configure the repo by hand, you should be able to get RPMs. At least this time, if work becomes overwhelming again, what has been done will remain accessible :-) I would prefer to not announce this officially just yet, but some feedback be nice (thus this email). So if you feel like testing and are facing problem, let me know! Hope this helps, Best regards, Pierre _______________________________________________ r-devel mailing list r-devel&lt; at &gt;lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2012-01-04T08:43:25 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/288 <pre>Good day everyone, As indicated on the planet, I just re-wrote almost completely R2spec, tried to make the code cleaner. This means that if you have code relying on it, it will most likely break with this update, but I hope you'll find the new code cleaner/easier to work with. On the other-side I added things like unit-tests so I am confident the code does what it's supposed to but I would appreciate if some of you had/took the time to test it. Feel free to shout any complains you may have, Thanks, Pierre Update are: F15: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc15 F16: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc16 EL5: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el5 EL6: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el6 _______________________________________________ r-devel mailing list r-devel&lt; at &gt;lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2011-11-12T20:38:30 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/285 <pre>Hi Tom, what are your plans for 2.14.0? I am asking in light of the development plan of R. Specifically, in this case, I am interested on the F-16 case. Regards, </pre> José Matos 2011-11-01T11:30:50 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/273 <pre> In R2spec-3.0.3-1, if you set a local source (-s &lt;source&gt;) then the URL and source0 fields in the spec will remain empty. Such specs fail to build. There are a variety of ways to address this, I'm not sure that what I've done is really a superior solution. in RPackage.py, down the branch of "I've only got a source, not a source0", I added self.source0 = source self.URL = source (see below). This means that URL is populated with a local file path, but that's really all that's available. .... All I'm really trying to do right now is get ggplot to one of my customers. I wasn't gearing up for contributing much code, but I can, if that's what Pierre-Yves wants. I have to say, this is being a distinctly frustrating process. .... "below"... def setSource(self, source0, source): ''' From the url retrieve the name of the source ''' if source != None and source0 != None: if source != source0.rsplit('/',1)[1] : sys.e</pre> Allen S. Rout 2011-04-12T20:42:51 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/270 <pre> The dependency resolution in R2spec introduces loops. Try to build foreach or iterators. In R2spec's calculation of deps, they depend on each other. This appears to be because R2spec promotes a 'suggests' to a 'depends'. This might be because the 'suggests' is used in the vigniettes? .... Argh. Package: iterators Type: Package Title: Iterator construct for R Version: 1.0.3 Author: REvolution Computing Maintainer: REvolution Computing &lt;packages-rppkj4QLs097ANvvEkjd4WoLBQzVVOGK&lt; at &gt;public.gmane.org&gt; Description: Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data. Depends: R (&gt;= 2.5.0), utils Suggests: foreach License: Apache License (== 2.0) Packaged: 2009-10-05 20:31:21 UTC; weston Repository: CRAN Date/Publication: 2009-10-06 06:56:52 Package: foreach Type: Package Title: Foreach looping construct for R Version: 1.3.0 Author: REvolution Computing Maintainer: REvolution Computing &lt;packages-rppkj4QLs097A</pre> Allen S. Rout 2011-04-12T19:27:08 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/269 <pre> When I try to build from a local source, it fails to find the source file. [root&lt; at &gt;troll-2 cran]# pwd /var/tmp/cran [root&lt; at &gt;troll-2 cran]# ls -l total 828 -rw-r--r-- 1 root root 308395 Dec 22 2009 DBI_0.2-5.tar.gz -rw-r--r-- 1 root root 518499 Apr 12 14:58 plyr_1.2.1.tar.gz -rwxr--r-- 1 root root 181 Apr 12 15:06 yadda -rw-r--r-- 1 root root 138 Apr 12 15:04 yadda~ [root&lt; at &gt;troll-2 cran]# R2rpm -s plyr_1.2.1.tar.gz Your source does not exist, please use the full path (plyr_1.2.1.tar.gz) [root&lt; at &gt;troll-2 cran]# R2rpm -s ./plyr_1.2.1.tar.gz Your source does not exist, please use the full path (./plyr_1.2.1.tar.gz) [root&lt; at &gt;troll-2 cran]# R2rpm -s /var/tmp/cran/plyr_1.2.1.tar.gz * Retrieve the source ************************************************** * Name of the packager = Allen Rout * Mail of the packager = asr-hnhdhkBXzx8&lt; at &gt;public.gmane.org ************************************************** * Name of the library = plyr * Version of the library = 1.2.1 * Summary of the library = Tools for splitting, applying a</pre> Allen S. Rout 2011-04-12T19:10:54 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/268 <pre>FYI :-) Pierre _______________________________________________ r-devel mailing list r-devel-TuqUDEhatI4ANWPb/1PvSmm0pvjS0E/A&lt; at &gt;public.gmane.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves Chibon 2011-02-25T16:21:11 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/266 <pre>Hi, I have submitted 4 new reviews which are (directly or not) needed update the R-GenomicFeatures package (which if not done will lead to a FTBFS at some point). R-Rcompression: https://bugzilla.redhat.com/show_bug.cgi?id=673658 R-RCurl: https://bugzilla.redhat.com/show_bug.cgi?id=673660 R-ALL: https://bugzilla.redhat.com/show_bug.cgi?id=673661 R-XML: https://bugzilla.redhat.com/show_bug.cgi?id=673665 Thanks for the help, Cheers, Pierre </pre> Pierre-Yves 2011-01-29T14:46:12 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/265 <pre>R 2.12.1 is built now for Fedora and EPEL. It is in "updates-testing" (or it will be within the next 24 hours). In accordance with the new policies on Fedora Updates, these new packages will not be pushed as official updates until they either receive positive testing from users, or sit in updates-testing for two weeks. You can help us test these packages, and move them forward. Here's how: 1. Go to the Fedora Updates web application (its real name is "Bodhi"): https://admin.fedoraproject.org/updates/ Once you're there, click the login blue box at the top left, and login with your Fedora Account. If you don't have a Fedora Account, you can give feedback, but it doesn't count towards giving the update positive karma. For that reason, I would strongly recommend that you take 45 seconds and create a Fedora Account. :) 2. Click on the link for the Fedora R test update that matches your release: Fedora 13: https://admin.fedoraproject.org/updates/rkward-0.5.4-2.fc13,rpy-2.0.8-6.fc13,R-2.12.1-1.fc13 Fedora 14</pre> Tom Callaway 2010-12-20T17:57:38 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/263 <pre>R 2.12.0 is built now for Fedora and EPEL. It is in "updates-testing" (or it will be within the next 24 hours). I did not do this build for Fedora 12, as that release will be End-Of-Life in a month. In accordance with the new policies on Fedora Updates, these new packages will not be pushed as official updates until they either receive positive testing from users, or sit in updates-testing for two weeks. You can help us test these packages, and move them forward. Here's how: 1. Go to the Fedora Updates web application (its real name is "Bodhi"): https://admin.fedoraproject.org/updates/ Once you're there, click the login blue box at the top left, and login with your Fedora Account. If you don't have a Fedora Account, you can skip this step. 2. Click on the link for the Fedora R test update that matches your release: Fedora 13: https://admin.fedoraproject.org/updates/rpy-2.0.8-5.fc13,R-2.12.0-1.fc13 Fedora 14: https://admin.fedoraproject.org/updates/rpy-2.1.7-1.fc14,R-2.12.0-1.fc14 EPEL-4 (RHEL-4): ht</pre> Tom "spot" Callaway 2010-11-02T20:49:51 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/262 <pre>Hi all, I just found out a new packages repository: http://www.omegahat.org It seems to contain some interesting libraries such as a Rgtk. Pierre </pre> Pierre-Yves 2010-10-28T11:11:22 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/261 <pre>Dear all, FYI, Remi has updated his scripts so we now have the following page summarizing the packages which need to be updated (+ the usual false positive). http://rpms.famillecollet.com/rpmphp/rpm.php?type=R&amp;what=%25work Regards, Pierre </pre> Pierre-Yves 2010-09-21T16:41:02 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/256 <pre>Hi, If someone could have a look at this review I would be pleased. I need it to update R-BSgenome which is needed for R-hgu95av2probe. https://bugzilla.redhat.com/show_bug.cgi?id=609079 This might be of some help to save time: http://pingou.fedorapeople.org/reviewHelper.py (comments are welcome of course) Thanks, Pierre </pre> Pierre-Yves 2010-07-01T09:16:22 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/255 <pre>R 2.11.1 is built now for Fedora and EPEL. It is in "updates-testing" (or it will be within the next 24 hours). It will likely be the last R update for Fedora 11. In accordance with the new policies on Fedora Updates, these new packages will not be pushed as official updates until they either receive positive testing from users, or sit in updates-testing for two weeks. You can help us test these packages, and move them forward. Here's how: 1. Go to the Fedora Updates web application (its real name is "Bodhi"): https://admin.fedoraproject.org/updates/ Once you're there, click the login blue box at the top left, and login with your Fedora Account. If you don't have a Fedora Account, you can skip this step. 2. Click on the link for the Fedora R test update that matches your release: Fedora 11: https://admin.fedoraproject.org/updates/rpy-2.0.8-3.fc11,R-2.11.1-1.fc11 Fedora 12: https://admin.fedoraproject.org/updates/rpy-2.0.8-3.fc12,R-2.11.1-1.fc12 Fedora 13: https://admin.fedoraproject.org/updates/rpy-</pre> Tom "spot" Callaway 2010-06-03T12:55:55 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/254 <pre> _______________________________________________ r-devel mailing list r-devel-TuqUDEhatI4ANWPb/1PvSmm0pvjS0E/A&lt; at &gt;public.gmane.org https://admin.fedoraproject.org/mailman/listinfo/r-devel</pre> Pierre-Yves 2010-05-31T09:36:00 http://comments.gmane.org/gmane.linux.redhat.fedora.r.devel/253 <pre>Hi all, As announced on my blog, I have released the new version of R2spec (version 3.0.0) containing R2rpm. Below[2] is the full changelog for this release. Thanks for your comments/feedbacks on this release. Feel free to test it again and add karma on Bodhi [1] Thanks to all of you again, Pierre [1] https://admin.fedoraproject.org/updates/R2spec-3.0.0-1.fc13 https://admin.fedoraproject.org/updates/R2spec-3.0.0-1.fc12 https://admin.fedoraproject.org/updates/R2spec-3.0.0-1.fc11 https://admin.fedoraproject.org/updates/R2spec-3.0.0-1.el4 https://admin.fedoraproject.org/updates/R2spec-3.0.0-1.el5 [2] Changelog: ---------- Version 3.0.0 -- 05th May 2019 - Features added * R2spec can now be called from an external script * Use template via jinja2 to generate the spec files (Based on an idea of Allen S. Rout) * Create the R2rpm script which directly builds the rpm * Add a man page for R2rpm * Add the -p option which enable to build a spec from a package name * Parse the PACKAGES file from the r</pre> Pierre-Yves 2010-05-05T12:52:53 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.linux.redhat.fedora.r.devel