[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
Dear Martin, Thank you for this clarification. I must admit that I did not realize that there exists now a 'git log' Snapshot Date, since usually the information: 'This page was generated on 2017-10-15 16:06:50 -0400 (Sun, 15 Oct 2017)' was sufficient for me. Best regards, Christian P.S.: Since there are still a couple of questions open, but maybe I have asked too many questions in this thread, I have decided to create a new thread for every question that I have (I hope these questions may be of general interest.)
On 10/16/17 04:00, Martin Morgan wrote:
On 10/15/2017 06:00 PM, cstrato wrote:
I have just seen the update 2017-10-15 of the BUILD/CHECK report: ??http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/ which was not available when I have sent my former mail. For some reason my commit to version xps_1.37.2 was not accepted. Please tell me what I need to do to solve this problem.
I guess you mean this commit xps master$ git log -n 1 commit d83779f467f7ac6736f95f4f8b78839654ab1af2 Author: rabbitus <rabbitus at lumimacs-iMac.local> Date:?? Sun Oct 15 13:52:26 2017 +0200 ??? update for configure.in which is where the version bump occurred xps master$ git show d83779f467f7ac6736f95f4f8b78839654ab1af2 DESCRIPTION commit d83779f467f7ac6736f95f4f8b78839654ab1af2 Author: rabbitus <rabbitus at lumimacs-iMac.local> Date:?? Sun Oct 15 13:52:26 2017 +0200 ??? update for configure.in diff --git a/DESCRIPTION b/DESCRIPTION index fb59243..af15fa0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ ?Package: xps -Version: 1.37.1 +Version: 1.37.2 ?Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays ???????? including Exon Arrays, Whole Genome Arrays and Plate Arrays ?Author: Christian Stratowa, Vienna, Austria As you know, bioconductor builds are NIGHTLY. The build report you cite has a snapshot date of 2017-10-14 17:00:13 -0400 (Sat, 14 Oct 2017) so your commit cam after the snapshot. Wait for the next build report. Martin
Best regards, Christian On 10/15/17 21:37, cstrato wrote:
Hi, Since 'https://github.com/cstrato/xps' does only contain information how to create or push a repository I tried to follow again: http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/ 2. View existing remotes $ git remote -v origin? git at github.com:cstrato/xps.git (fetch) origin? git at github.com:cstrato/xps.git (push) upstream??????? git at git.bioconductor.org:packages/xps.git (fetch) upstream??????? git at git.bioconductor.org:packages/xps.git (push) 3. Make and commit changes to the master branch $ git checkout master M?????? DESCRIPTION M?????? NEWS M?????? configure.in Already on 'master' Your branch is up-to-date with 'origin/master'. # edit files, etc. $ git add -v DESCRIPTION $ git add -v NEWS $ git add -v configure.in When running 'commit' I got the following information, which is not clear to me: $ git commit -m "update for configure.in" [master 7a9855f] update for configure.in ??Committer: rabbitus <rabbitus at lumimacs-iMac.local> Your name and email address were configured automatically based on your username and hostname. Please check that they are accurate. You can suppress this message by setting them explicitly. Run the following command and follow the instructions in your editor to edit your configuration file: ???? git config --global --edit After doing this, you may fix the identity used for this commit with: ???? git commit --amend --reset-author ??3 files changed, 62 insertions(+), 58 deletions(-) So I tried: $ git config --global --edit # This is Git's per-user configuration file. [user] # Please adapt and uncomment the following lines: #?????? name = rabbitus #?????? email = rabbitus at lumimacs-iMac.local and changed the '.gitconfig' file to: # This is Git's per-user configuration file. [user] # Please adapt and uncomment the following lines: #?????? name = cstrato #?????? email = cstrato at aon.at It is not clear to me whether I have to change my name/email or keep the original one. Could you tell me which one should be the correct one? Then I did run: $ git commit --amend --reset-author # Please enter the commit message for your changes. Lines starting # with '#' will be ignored, and an empty message aborts the commit. # # Committer: rabbitus <rabbitus at lumimacs-iMac.local> # # On branch master # Your branch is ahead of 'origin/master' by 1 commit. #?? (use "git push" to publish your local commits) # # Changes to be committed: #?????? modified:?? DESCRIPTION #?????? modified:?? NEWS #?????? modified:?? configure.in In this case I did not change anything, since I am not sure what it means. Can you explain what this means, since 'https://git-scm.com/docs/git-commit' did not help me. Should I change this file? Then I did steps 5 and 6 and got the following: 5. Push updates to GitHub's (origin) master branch $ git push origin master Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. 6. Next, push updates to Bioconductor's (upstream) master branch $ git push upstream master Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': Counting objects: 5, done. Delta compression using up to 8 threads. Compressing objects: 100% (5/5), done. Writing objects: 100% (5/5), 727 bytes | 0 bytes/s, done. Total 5 (delta 4), reused 0 (delta 0) To git.bioconductor.org:packages/xps.git ??? d63ffaf..d83779f? master -> master Finally I did: $ ssh -v git at git.bioconductor.org/packages/xps OpenSSH_7.4p1, LibreSSL 2.5.0 debug1: Reading configuration data /Users/rabbitus/.ssh/config debug1: Reading configuration data /etc/ssh/ssh_config ssh: Could not resolve hostname git: nodename nor servname provided, or not known However, now I get only an ssh error message: Do you know what I did wrong this time? Thank you. Best regards, Christian On 10/13/17 20:12, Turaga, Nitesh wrote:
Hi, Both your `origin` and `upstream` are set to the same location i.e git at git.bioconductor.org:packages/xps. This is wrong. You want your origin to point to `git at github.com:cstrato/xps` You can do this by following the commands, ????`git remote set-url origin git at github.com:cstrato/xps.git` ????`git push origin master` All of this documentation is given in bioconductor.org/developers/how-to/git/. Best, Nitesh
On Oct 13, 2017, at 2:07 PM, cstrato <cstrato at aon.at> wrote: Dear Martin, Following your advice https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ I did the following: $ cd xps $ git remote add upstream git at git.bioconductor.org:packages/xps.git $ git fetch upstream Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': ?From git.bioconductor.org:packages/xps * [new branch]????? RELEASE_2_10 -> upstream/RELEASE_2_10 * [new branch]????? RELEASE_2_11 -> upstream/RELEASE_2_11 * [new branch]????? RELEASE_2_12 -> upstream/RELEASE_2_12 * [new branch]????? RELEASE_2_13 -> upstream/RELEASE_2_13 * [new branch]????? RELEASE_2_14 -> upstream/RELEASE_2_14 * [new branch]????? RELEASE_2_2 -> upstream/RELEASE_2_2 * [new branch]????? RELEASE_2_3 -> upstream/RELEASE_2_3 * [new branch]????? RELEASE_2_4 -> upstream/RELEASE_2_4 * [new branch]????? RELEASE_2_5 -> upstream/RELEASE_2_5 * [new branch]????? RELEASE_2_6 -> upstream/RELEASE_2_6 * [new branch]????? RELEASE_2_7 -> upstream/RELEASE_2_7 * [new branch]????? RELEASE_2_8 -> upstream/RELEASE_2_8 * [new branch]????? RELEASE_2_9 -> upstream/RELEASE_2_9 * [new branch]????? RELEASE_3_0 -> upstream/RELEASE_3_0 * [new branch]????? RELEASE_3_1 -> upstream/RELEASE_3_1 * [new branch]????? RELEASE_3_2 -> upstream/RELEASE_3_2 * [new branch]????? RELEASE_3_3 -> upstream/RELEASE_3_3 * [new branch]????? RELEASE_3_4 -> upstream/RELEASE_3_4 * [new branch]????? RELEASE_3_5 -> upstream/RELEASE_3_5 * [new branch]????? master???? -> upstream/master $ git fetch upstream Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': $ git merge upstream/master Already up-to-date. $ git push origin master Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': Everything up-to-date $ git remote -v origin? git at git.bioconductor.org:packages/xps (fetch) origin? git at git.bioconductor.org:packages/xps (push) upstream??????? git at git.bioconductor.org:packages/xps.git (fetch) upstream??????? git at git.bioconductor.org:packages/xps.git (push) $ git checkout master M?????? DESCRIPTION M?????? NEWS M?????? configure.in Already on 'master' Your branch is up-to-date with 'origin/master'. $ git add -v DESCRIPTION add 'DESCRIPTION' $ git add -v NEWS add 'NEWS' $ git add -v configure.in add 'configure.in' $ git push origin master Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': Everything up-to-date $ git push upstream master Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': Everything up-to-date I hope that I could commit my changes and my development version on ?? https://github.com/cstrato/xps will be updated to 'xps_1.37.2' (PS: my repository https://github.com/cstrato/xps is still empty) Thank you very much for your help. Best regards, Christian On 10/12/17 23:21, Martin Morgan wrote:
On 10/12/2017 04:13 PM, cstrato wrote:
Dear Martin, Thank you for your informative reply. 1, My SSH public key that you mentioned is the correct one. 2, After following your advice and running ??? ssh -v git at git.bioconductor.org I got: OpenSSH_7.4p1, LibreSSL 2.5.0 debug1: Reading configuration data /etc/ssh/ssh_config debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22. debug1: Connection established. debug1: identity file /Users/rabbitus/.ssh/id_rsa type 1 debug1: key_load_public: No such file or directory ... debug1: Remote: PTY allocation disabled. PTY allocation request failed on channel 0 hello c.stratowa, this is git at ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.13.0 ... bash: debug1:: command not found 3, Nevertheless, I could run: ??? git clone git at git.bioconductor.org:packages/xps I got: Cloning into 'xps'... Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa': remote: Counting objects: 2757, done. remote: Compressing objects: 100% (2741/2741), done. remote: Total 2757 (delta 2077), reused 0 (delta 0) Receiving objects: 100% (2757/2757), 5.62 MiB | 945.00 KiB/s, done. Resolving deltas: 100% (2077/2077), done. Checking connectivity... done.
?From the Bioconductor perspective, I think you are 'good to go',
and you could follow, e.g.,
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
to commit and push changes to the Bioconductor git repository.
These changes would be incorporated into the nightly builds, etc.,
as before.
4, In 'https://github.com/settings/keys' I deleted the old SSH key and tried to add a new SSH key, where in 'Key' I copied once again my public 'id_rsa'. However, once again I received an email with the wrong key 'df:2d:78:4f:**'
This is the 'fingerprint' of the SSH public key, rather than the public key itself.
I do not understand why my correct key is not accepted. According to 'https://caius.github.io/github_id/' my user id is: cstrato is github user #32616897 My public key at 'https://github.com/cstrato.keys' is still empty.
I don't know the answer to this github question; maybe public keys are not displayed by default? At any rate it 'does not matter'; github allows you to clone via https + password, or via ssh; all you need is to be able to clone your newly created, empty github xps repository, which it seems from below that you can. It sounds like, now that you have access to git.bioconductor.org, you could follow https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Martin
I am not sure what I need to do next? Thank you. Best regards, Christian On 10/12/17 19:40, Martin Morgan wrote:
On 10/08/2017 01:37 PM, cstrato wrote:
Dear all, I wanted to update my package 'xps' and realized that I can no longer use 'svn commit' In order to use GIT I did the following: 1, I created a public key '~/.ssh/id_rsa.pub' 2, I did submit my 'SSH public key or github id to Bioconductor', using the 'git/svn transition: ssh keys' form. Here I entered my SVN user id, but it was not clear what my ID is. So I checked 'svn info' and used? first my name 'c.stratowa' as SVN user id. Since I did not succeed I repeated the procedure and used the UUID as SVN user id. Is this correct, or how do I get my SVN user id? 3, I created a new GitHub repository: https://github.com/cstrato/xps 4, Then I tried to clone the empty repository from GitHub. Here is the result: iMac:GIT cstrato$ git clone https://github.com/cstrato/xps.git Cloning into 'xps'... warning: You appear to have cloned an empty repository. Checking connectivity... done. iMac:GIT cstrato$ git clone https://github.com/cstrato/xps.git fatal: destination path 'xps' already exists and is not an empty directory. iMac:GIT cstrato$ cd xps iMac:xps cstrato$ git remote add upstream git at git.bioconductor.org:packages/xps.git iMac:xps cstrato$ git fetch upstream Permission denied (publickey). fatal: Could not read from remote repository.
there's a single public key associated with access to xps, ending with ??? /m+bdjnFrDw5Fod8Sa9zDh2vXcICrNcxWGds2rbG3Q== that should correspond to one of the public keys in your ~/.ssh/ directory. If not, resubmit the form with You can try ??? ssh -v git at git.bioconductor.org and try to diagnosis why this public key is not being matched; a possibility is FAQ #15 where git is choosing the wrong key ??? https://bioconductor.org/developers/how-to/git/faq/
Please make sure you have the correct access rights and the repository exists. 5, I realized that I needed to add my public key to: https://github.com/settings/keys The email I got was: The following SSH key was added to your account: iMac df:2d:**:**:** etc
no, that doesn't look like an ssh key, it looks like a MAC address. What's you're github user id? the link https://github.com/settings/keys is only useful to you. My public key is at https://github.com/mtmorgan.keys
If you believe this key was added in error, you can remove the key and disable access at the following location: https://github.com/settings/keys Now my questions are: Do you think the SSH key should look as the one I got? What did I do wrong? Why do I get: permission denied? Thank you. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n?? S.t.r.a.t.o.w.a V.i.e.n.n.a?????????? A.u.s.t.r.i.a e.m.a.i.l:??????? cstrato at aon.at _._._._._._._._._._._._._._._._._._
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