Re: [MoM] Re: ITP: r-cran-igraph -- GNU R package for igraph
Hi Alba, On Fri, May 15, 2015 at 11:56:28AM +0100, Alba Crespi wrote: > > Aaaarg, for sure that's OK. My bad! Git-buildpackage recently changed > > its interface and droped the deprecated "git" in favour of consistently > > using gbp. I had assumed that I changed every occurance in the policy > > but I did not and even worse copied it blindly. Sorry for this - its > > fixed now. > > Excellent! Hmm, well, I'd call this rather stupid than excellent ... but I know what you mean. ;-) > > > > both on the very same tarball without the need to download anything in > > > > addition. So could you please import and push this? > > > > > > Sorry, I'm not sure what exactly I have to push? > > > > git push --all --set-upstream > > git push --tags Pristine-tar branch arrived in the remote repository and I'm now able to `gbp buildpackage`. > > > > * Initial release. (Closes: #784264) > > > > > > > > -- Alba Crespi Mon, 04 May 2015 > > 18:56:30 > > > > +0100 > > > > > > > > ... perhaps by updating the timestamp. > > > > > > done > > > > > > > > > > > > > > Regarding debian/control: You mention > > > > > > > >Testsuite: autopkgtest > > > > > > > > This is probably a cut-n-pasto since no testsuite is actually provided. > > > > While we try to approach test suites for each package the upstream code > > > > does not seem to provide anything that might be useful for this. In > > any > > > > case you can even drop this field since it is automatically added by > > > > dpkg-buildpackage if a test suite is found. > > > > > > Ok, deleted it. (When I was doing this, I followed the instructions on > > the > > > debian-med web page) > > > > > > > > > > The file debian/gbp.conf could be dropped IMHO. It doese not specify > > > > anything non standard and unneeded files might add noise. BTW, it > > > > specifies pristine-tar = True which is wrong at the moment. > > > > > > Drop it. > > > > Fine. I guess if you push for pristine-tar I will be able to see all > > this. Hmmm, I can not see these changes in the repository. Master remains at $ git log commit 1d325dd0667ab3111501693ef4d9428b49c05301 Author: Alba Crespi Date: Tue May 12 16:13:29 2015 +0100 Imported Debian patch 1.0-4-3 > > Just `git push`. > > > > I'd like to also comment that when I reproduce all the steps for another > package, r-cran-nnls, it gives me different errors. The first ones is this: > > gbp import-orig --pristine-tar ~/r-cran-nnls/ I think this should rather be gbp import-orig --pristine-tar /r-cran-nnls_1.4.orig.tar.gz > What will be the source package name? [] r-cran-nnls > What is the upstream version? [] 1.4 > gbp:error: The orig tarball contains .git metadata - giving up. Seems you pointed import-orig not to the orig.tar.gz *file* but rather to the git repository where the tarball should be imported into (which for sure contains a .git dir. > Oh, and another curious thing that happened and I don't understand why, I > reproduced all the steps once more and worked, any ideas of why now and not > before? To be honest I didn't do anything conciously different... > And apparently nnls, maybe there is not everything in git? or at least not > that I see? No, just a usual tarball from cran as far as I can see. > And I can't see where is the new version of r-cran-fastmatch. I can't parse this, sorry. Please commit and push the changes you did and I'll have a look. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150515133358.gd14...@an3as.eu
Re: [MoM] Re: ITP: r-cran-igraph -- GNU R package for igraph
Hi Alba, On Thu, May 14, 2015 at 10:34:28PM +0100, Alba Crespi wrote: > > Since you are quite advanced and I assume not much mentoring will be > > needed any more (same with the other student Afif I hope to be able to > > work with you both at the same time and the usual mentoring quality (in > > terms of speedy response and detailed explanations). I hope you like > > this. > > It sounds great! :-) > > Our policy says that we are using a workflow that includes a > > pristine-tar branch. You can create this as written in policy by > > using > > > > git import-orig --pristine-tar /path/to/package_version.orig.tar.gz > > > > Apparently, import-orig is not an option for my version of git? It doesn't > appear in the list of possible commands... > > git import-orig --pristine-tar r-cran-fastmatch_1.0-4.orig.tar.gz > git: 'import-orig' is not a git command. See 'git --help'. > > However, I could do by doing: gbp import-orig --pristine-tar > /path/.orig.tar.gz. Is that ok? Aaaarg, for sure that's OK. My bad! Git-buildpackage recently changed its interface and droped the deprecated "git" in favour of consistently using gbp. I had assumed that I changed every occurance in the policy but I did not and even worse copied it blindly. Sorry for this - its fixed now. > > You can do this also now in the current state of the repository. The > > rationale behind this branch is that it contains the necessary metadata > > to recreate a md5 sum identical tarball. This makes sure we are working > > both on the very same tarball without the need to download anything in > > addition. So could you please import and push this? > > Sorry, I'm not sure what exactly I have to push? git push --all --set-upstream git push --tags > > * Initial release. (Closes: #784264) > > > > -- Alba Crespi Mon, 04 May 2015 18:56:30 > > +0100 > > > > ... perhaps by updating the timestamp. > > done > > > > > > Regarding debian/control: You mention > > > >Testsuite: autopkgtest > > > > This is probably a cut-n-pasto since no testsuite is actually provided. > > While we try to approach test suites for each package the upstream code > > does not seem to provide anything that might be useful for this. In any > > case you can even drop this field since it is automatically added by > > dpkg-buildpackage if a test suite is found. > > Ok, deleted it. (When I was doing this, I followed the instructions on the > debian-med web page) > > > > The file debian/gbp.conf could be dropped IMHO. It doese not specify > > anything non standard and unneeded files might add noise. BTW, it > > specifies pristine-tar = True which is wrong at the moment. > > Drop it. Fine. I guess if you push for pristine-tar I will be able to see all this. > > Everything else looks fine to me. > > Excellent news then! :) > > Just one more question for now: once I have done the changes, and re-build > the package, I have to commit the package in the same way as I did the > first time or do I need to use a different set of commands? Just `git push`. Thanks for your work on this Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150515054100.ga14...@an3as.eu
[MoM] Re: ITP: r-cran-igraph -- GNU R package for igraph
Dear Alba, On Thu, May 14, 2015 at 12:20:04PM +0100, Alba Crespi wrote: > > I have seen one repository created by the user albac-guest with the name > > pkg.git. It seems you literally followed: > > > > ssh git.debian.org > > cd /git/debian-med > > ./setup-repository pkg 'Packaging of pkg in Debian' > > > > while this "pkg" was just a placeholder for your package. I now tried to > > enhance the syntax to > > > > ./setup-repository 'Packaging of in Debian' > > That sound much clear to me! Thanks :) :-) Since we are now diving into the details of the Debian Med team and I would really encourage you to keep on asking even if the questions you might come up might sound simple I suggest we follow the formalism I established in the Debian Med team which is called "Mentoring of the Month": https://wiki.debian.org/DebianMed/MoM These mail exchanges are exactly what MoM is about and so I took the freedom without asking you to add an according row to the MoM students table and tagged the subject [MoM]. This has the advantage that other potential newcomers will be able to easily spot this type of conversation while people who are just keen on discussing medical software might skip this. You might have noticed that I have put you into the June slot. The reason is that one one hand May is just occupied but I'll be basically offline in June and I would really get you up and running quite quickly. Since you are quite advanced and I assume not much mentoring will be needed any more (same with the other student Afif I hope to be able to work with you both at the same time and the usual mentoring quality (in terms of speedy response and detailed explanations). I hope you like this. > > We are really happy about hints like this. However, the problem is from > > a perspective of a senior developer it is sometimes hard to feel like a > > newcomer and what needs to be mentioned in what detail. Any hint you > > might like to give how to enhance the documentation after you understood > > things due to some explanation here on the list would be welcome. > > As you said, once I understand better, I will This would be really welcome. BTW, the policy document remains in SVN[1] which might a show stopper for some Git users. We might consider moving the document (and the other files in the community dir to Git) if others agree. In any case you also have commit permissions to SVN. > > (and here replace by r-cran-fastmatch) via > > > > git push --all --set-upstream > > git push --tags > > Done it! Great. I just pulled it. > Yes, I am subscribed to the list. OK, so I only write to the list. Here are my comments to the r-cran-fastmatch packaging. Our policy says that we are using a workflow that includes a pristine-tar branch. You can create this as written in policy by using git import-orig --pristine-tar /path/to/package_version.orig.tar.gz You can do this also now in the current state of the repository. The rationale behind this branch is that it contains the necessary metadata to recreate a md5 sum identical tarball. This makes sure we are working both on the very same tarball without the need to download anything in addition. So could you please import and push this? Regarding debian/changelog you have created three different paragraphs which might describe your changes. This is not necessary for not yet uploaded files. I guess you have uploaded these revisions to mentors.d.n but this is irrelevant for the final upload since neither 1.0-4-1 nor (1.0-4-2 were really uploaded to unstable the changelog might be confusing. Moreover the ITP bug is closed in an outdated changelog paragraph - so it will not effectively closed by the upload. Finally ftpmaster who needs to accept the package does not like long "uninteresting" stories. In short: Please strip down the changelog to only r-cran-fastmatch (1.0-4-1) unstable; urgency=medium * Initial release. (Closes: #784264) -- Alba Crespi Mon, 04 May 2015 18:56:30 +0100 ... perhaps by updating the timestamp. Regarding debian/control: You mention Testsuite: autopkgtest This is probably a cut-n-pasto since no testsuite is actually provided. While we try to approach test suites for each package the upstream code does not seem to provide anything that might be useful for this. In any case you can even drop this field since it is automatically added by dpkg-buildpackage if a test suite is found. The file debian/gbp.conf could be dropped IMHO. It doese not specify anything non standard and unneeded files might add noise. BTW, it specifies pristine-tar = True which is wrong at the moment. Everything else looks fine to me. > Thank you very much! You are welcome. :-) Welcome in the Debian Med team Andreas. [1] https://anonscm.debian.org/viewvc/debian-med/trunk/community/website/docs/policy.xml?view=markup -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a sub
Re: ITP: r-cran-igraph -- GNU R package for igraph
Hi Andreas, > > I think at this part of the policy are the helpful hints: > > > > > >https://debian-med.alioth.debian.org/docs/policy.html#git-tips > > > > > > If you have some more specific question where you might get struck > please > > > give more details where you specifically might need any help. > > > > Sorry, but I find the information rather confusing. > > I created an ssh key, I copied to my alioth acount and ssh to > git.debian.org > > and setup the repository. > > I have seen one repository created by the user albac-guest with the name > pkg.git. It seems you literally followed: > > ssh git.debian.org > cd /git/debian-med > ./setup-repository pkg 'Packaging of pkg in Debian' > > while this "pkg" was just a placeholder for your package. I now tried to > enhance the syntax to > > ./setup-repository 'Packaging of in Debian' > That sound much clear to me! Thanks :) > Do you think this is better? Since I did not know with what exact package > you wanted to start I did on git.debian.org now: > > ./setup-repository r-cran-fastmatch 'Packaging of r-cran-fastmatch in > Debian' > > Please do so for the other packages you want to create. > Perfect :) > > (I would like to comment that for new members it is quite hard find how > to > > do all this steps, maybe a good improvement for debian-med would be to > have > > a simplier instrucctions and step by step, even the most obvious ones for > > the seniors developers could be a great advantage to get started!) > > We are really happy about hints like this. However, the problem is from > a perspective of a senior developer it is sometimes hard to feel like a > newcomer and what needs to be mentioned in what detail. Any hint you > might like to give how to enhance the documentation after you understood > things due to some explanation here on the list would be welcome. > As you said, once I understand better, I will > > > From here on I don't understand how to use git to upload my packages: > > I understand that somewhere I need to create a directory where to upload > > the package? How? Where? > > You do not upload any package from the Git repository. You just commit > your packaging to the repository and the sponsor will pull from there, > check and upload. > > You should push your local packaging repository after > > git remote add origin git+ssh://git.debian.org/git/debian-med/.git > > (and here replace by r-cran-fastmatch) via > > git push --all --set-upstream > git push --tags > Done it! > > > Do I have to build the package in the repository or locally and then > upload > > it? > > The repository is just to develop the packaging. There is no direct > upload process done from the Git repository. > > > Thank you very much, > > Hope this helps - feel free to keep on asking > > Andreas. > > PS: If you could confirm that you are subscribed to the Debian Med mailing > list I would stop CCing you - which is the usual list policy. > Yes, I am subscribed to the list. Thank you very much! Alba
Re: ITP: r-cran-igraph -- GNU R package for igraph
Hi Alba, On Wed, May 13, 2015 at 06:51:21PM +0100, Alba Crespi wrote: > > Remark: The section concept is from the very early days of Debian and > > has its flaws - in this case that only one section can be specified. > > I put the section back to gnu-r. Now lintian seems to be happy :) :-) > > I think at this part of the policy are the helpful hints: > > > >https://debian-med.alioth.debian.org/docs/policy.html#git-tips > > > > If you have some more specific question where you might get struck please > > give more details where you specifically might need any help. > > Sorry, but I find the information rather confusing. > I created an ssh key, I copied to my alioth acount and ssh to git.debian.org > and setup the repository. I have seen one repository created by the user albac-guest with the name pkg.git. It seems you literally followed: ssh git.debian.org cd /git/debian-med ./setup-repository pkg 'Packaging of pkg in Debian' while this "pkg" was just a placeholder for your package. I now tried to enhance the syntax to ./setup-repository 'Packaging of in Debian' Do you think this is better? Since I did not know with what exact package you wanted to start I did on git.debian.org now: ./setup-repository r-cran-fastmatch 'Packaging of r-cran-fastmatch in Debian' Please do so for the other packages you want to create. > (I would like to comment that for new members it is quite hard find how to > do all this steps, maybe a good improvement for debian-med would be to have > a simplier instrucctions and step by step, even the most obvious ones for > the seniors developers could be a great advantage to get started!) We are really happy about hints like this. However, the problem is from a perspective of a senior developer it is sometimes hard to feel like a newcomer and what needs to be mentioned in what detail. Any hint you might like to give how to enhance the documentation after you understood things due to some explanation here on the list would be welcome. > From here on I don't understand how to use git to upload my packages: > I understand that somewhere I need to create a directory where to upload > the package? How? Where? You do not upload any package from the Git repository. You just commit your packaging to the repository and the sponsor will pull from there, check and upload. You should push your local packaging repository after git remote add origin git+ssh://git.debian.org/git/debian-med/.git (and here replace by r-cran-fastmatch) via git push --all --set-upstream git push --tags > Do I have to build the package in the repository or locally and then upload > it? The repository is just to develop the packaging. There is no direct upload process done from the Git repository. > Thank you very much, Hope this helps - feel free to keep on asking Andreas. PS: If you could confirm that you are subscribed to the Debian Med mailing list I would stop CCing you - which is the usual list policy. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150514053006.gb14...@an3as.eu
Re: ITP: r-cran-igraph -- GNU R package for igraph
Hi Alba, On Tue, May 12, 2015 at 05:18:03PM +0100, Alba Crespi wrote: > > list and I take the freedom to do so here since the content is not > > really private and deserves updating in public. I hope you don't mind. > > Using the address that is the ITP owner might help you sorting this > > mail properly.] > > No problem! :-) > I'm trying to update the packages following the debian-med rules and I have > some questions: > > - When updated the section to 'science', lintian sugguests 'gnu-r'. Which > is the correct one? >From a neutral point of view the packages might fit into both sections. Debian policy says R packages should be in section gnu-r (that's why lintian is telling you this) ... and so Debian policy overrides what we said (for all packages which have no clear specification per Debian poplicy). May be this should be clarified. As a general rule: We try to get lintian clean packages - so follow lintian. Remark: The section concept is from the very early days of Debian and has its flaws - in this case that only one section can be specified. > W: r-cran-fastmatch: wrong-section-according-to-package-name > r-cran-fastmatch => gnu-r > > - What should I do with the ITP bugs that I opened for r-cran-fastmatch, > r-cran-nnls and r-cran-phangorn? Is the same system in debian-med? Do I > nedd another ITP for debian-med? No. Debian Med *is* Debian. We are just a team inside Debian. Just keep your ITPs. > > While these packages are not really medicine specific we usually also > > maintain the necessary preconditions. This helps us using all our > > quality assurance tools and help to respond quickly. For instance if a > > team member might notice that a package needs to be updated it happens > > that it is just done. If you remain a single maintainer this goes > > unnoticed. For instance r-cran-igraph is a similar example why it is in > > the Debian Med team. > > > > So there are quite good reasons (I could give even more) to stick to the > > team maintenance and I have a personal policy to sponsor only team > > maintained packages (and I have also good reasons for it). And I also > > sponsor from the team VCS rather than mentors. So while uploading to > > mentors is OK but not required. But if you want to get the packages > > sponsored by a Debian Med team member please commit to our VCS. If you > > need any help how to do this we will luckily help you approaching this. > > Yes please, I need some more information, I don't know how to do it. I think at this part of the policy are the helpful hints: https://debian-med.alioth.debian.org/docs/policy.html#git-tips If you have some more specific question where you might get struck please give more details where you specifically might need any help. Thanks for working on these packages Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150512163317.ga1...@an3as.eu
Re: ITP: r-cran-igraph -- GNU R package for igraph
[I think I have warned you that I would move private mails to our team list and I take the freedom to do so here since the content is not really private and deserves updating in public. I hope you don't mind. Using the address that is the ITP owner might help you sorting this mail properly.] Hi Alba, On Thu, May 07, 2015 at 04:08:02PM +0100, Alba Crespi wrote: > Sorry for not answering you before, but until this week I was quite busy. Fair enough - no problem for me. > This week I was working again with the debian packaging. > > First of all I would like to thank you for the igraph package, it seems > working fine! You are welcome. > So, so far I started with the phangorn dependencies that weren't in debian > (r-cran-fastmatch and r-cran-nnls) and I have uploaded to the debian > mentors. And I am currently waiting for sponsor. I don't know if this > should be part of the debian Med as well? While these packages are not really medicine specific we usually also maintain the necessary preconditions. This helps us using all our quality assurance tools and help to respond quickly. For instance if a team member might notice that a package needs to be updated it happens that it is just done. If you remain a single maintainer this goes unnoticed. For instance r-cran-igraph is a similar example why it is in the Debian Med team. So there are quite good reasons (I could give even more) to stick to the team maintenance and I have a personal policy to sponsor only team maintained packages (and I have also good reasons for it). And I also sponsor from the team VCS rather than mentors. So while uploading to mentors is OK but not required. But if you want to get the packages sponsored by a Debian Med team member please commit to our VCS. If you need any help how to do this we will luckily help you approaching this. > An I guess that soon I will also have the r-cran-phangorn package ready. My > question is if I should upload it in debian mentors as I did with the other > two or should I do something different for becoming part of debian Med? As I wrote below I have just added you to the Alioth team. This grants you commit permissions to Git and SVN. Our team policy https://debian-med.alioth.debian.org/docs/policy.html should have sufficient description how to work with these repositories. If not ... please ask here and we try to sort out any problem as quick as possible. Kind regards and thanks for working on these packages Andreas. > 2015-05-07 7:14 GMT+01:00 Andreas Tille : > > > Hi Alba, > > > > its more than a month ago since we exchanged mails. I have not seen any > > commits of your code to a the Debian Med VCS. Please keep me informed > > about any trouble you might have. The Debian Med team is very keen on > > helping you to finalise your package. > > > > Kind regards > > > > Andreas. > > > > On Sun, Apr 05, 2015 at 09:05:32AM +0200, Andreas Tille wrote: > > > Hi Alba, > > > > > > uhmm, your mail endet up in my SPAM folder - one more good reason to > > > post to the public list to make sure your mail will be found soon by a > > > responsible person. [So I keep the Debian Med developer list in CC :-)] > > > > > > On Thu, Apr 02, 2015 at 12:55:42PM +0200, Alba Crespi wrote: > > > > Hi, > > > > > > > > 2015-04-01 6:43 GMT+02:00 Andreas Tille : > > > > > > > > > I'm fine with this but could you please maintain phangorn in the > > Debian > > > > > Med team? I have not found any Alioth login of yours > > > > > > > > > > > > > My alioth login is "albac-guest". > > > > > > Added to Debian Med. > > > > > > > I am happy in principle to join the > > > > Debian Med team, but until now I have never used git, so I will need to > > > > learn some new things to participate fully. > > > > > > In Debian Med we also support the option to use SVN at your preference. > > > > > > > This is also my first time > > > > making Debian packages, so I think I need to start with one thing at a > > > > time. :) > > > > > > While I also subscribe to the do one thing at one time I think using a > > > Version Control System is evident for proper Debian package maintenance. > > > Regarding learning Debian packaging you are really welcome in the Debian > > > Med team since we have a good record in teaching newcomers. You might > > > like to consider joining "Mentoring of the Month" > > > > > > https://wiki.debian.org/DebianMed/MoM > > > > > > and since it involves any kind of questions the usage of Git or SVN is > > > included. :-) > > > > > > > When do you think that you will have time to upload an r-cran-igraph > > > > package? > > > > > > Its in the new queue but new processing is currently quite low (which is > > > probably due to the freeze of Jessie. I hope that it will be faster > > > again after the Jessie release.) > > > > > > Hope this helps > > > > > > Andreas. > > > > > > -- > > > http://fam-tille.de > > > > -- > > http://fam-tille.de > > -- http://fam-tille.de -- To U
