[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
cstrato
cstrato at aon.at
Mon Oct 16 20:23:27 CEST 2017
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
>>>>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>
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>>>>>
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>
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