[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
Martin Morgan
martin.morgan at roswellpark.org
Mon Oct 16 04:00:58 CEST 2017
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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