[Bioc-devel] Update data in data package, pcxnData
Sokratis Kariotis
s.kariotis at sheffield.ac.uk
Thu Mar 29 12:49:47 CEST 2018
Hey all,
The packages' changes went through to the 3_6 branch, but since pcxn and
pcxnData depend on each other, there are errors when they get built as they
see the old version of the other package. In the current example:
https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.htm
l , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now located in
the new pcxnData package but during build the old pcxnData is being used
and the error occurs since the file is not there. I have checked both
packages locally and they work when both are in their updated form. How can
we bypass this? Thanks.
Cheers,
Sokratis
On 27 March 2018 at 14:02, Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
wrote:
> Hey all,
>
> Thanks for the advice. I managed to fix the problem of no permissions! My
> windows machine, after an update, changed the paths to my github keys and
> had to reposition them. I have now succesfully pushed in both master and
> RELEASE_3_6 branches.
>
> Cheers,
> Sokratis
>
> On 26 March 2018 at 15:47, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
> wrote:
>
>> Hi Sokratis,
>>
>> Your key(s) on file is
>>
>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp
>> +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0
>> Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL
>> xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1
>> CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/Ujrr
>> XanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLu
>> nUjQpVwqrnlHXcRGjkLB
>>
>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+Q
>> V5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6n
>> FfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+
>> rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80T
>> a0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJ
>> Yw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd
>>
>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkB
>> CHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2
>> CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0
>> UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR
>> 2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8
>> cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf
>>
>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRt
>> Kf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/W
>> Z02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbvoZ3b9oPakFbQFiAtjPkN6h4
>> drr+iQq4to4jc5wvYw07uqIEEG8nZfiB+QWa5s+rplTS3zJZzr7xpEDT/7ZH
>> pKVduZUg34tzaN4+vONgofgOthUMWArO3oO69wPwAdoAUACRmXT02xknrcWZ
>> m4UtuhzT98FHLznSowZMLG3jm8vKgsgbH8UGGtz478UZW5xE4qS5LHiKJbcZ
>> FBCLFABUjCajuYF3z+bZF0cxbT9d+25kpp/p89lvljsvlE7vbxdqFmeobGS
>> Q6ftDq5btdEHfD2rc++iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9
>> sBL5gLFHTkl3KyxNdIsH9j0iNFdJmEHySZh2ePdrqG7ZE/FOKf77XTX+
>> acqgydF+Dsep16lTIxk94MXLk7Sz2v8XQqFtETa5q0Gkm70Ok/qht/O80nWU
>> T3QX44sPM4ivPckOHwnZjywpZyBONas26hP0M1pZSEvB5qLCMKyD4YmTJ5aZ
>> keCHh6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ==
>>
>> Are you sure you are using a private key which corresponds to any of
>> these public keys? I’d start with that.
>>
>> Best
>>
>> Nitesh
>>
>>
>> > On Mar 23, 2018, at 8:20 AM, Sokratis Kariotis <
>> s.kariotis at sheffield.ac.uk> wrote:
>> >
>> > Hey Lori,
>> >
>> > While under the RELEASE_3_6 branch and using git fetch upstream or git
>> push
>> > upstream/RELEASE_3_6:
>> >
>> >
>> >
>> >
>> >
>> >
>> > *Warning: Permanently added 'git.bioconductor.org
>> > <http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of
>> known
>> > hosts.Permission denied (publickey).fatal: Could not read from remote
>> > repository.Please make sure you have the correct access rightsand the
>> > repository exists.*
>> >
>> >
>> > git remove -v results to:
>> >
>> >
>> >
>> >
>> >
>> >
>> > *origin https://github.com/hidelab/pcxn.git
>> > <https://github.com/hidelab/pcxn.git> (fetch)origin
>> > https://github.com/hidelab/pcxn.git <https://github.com/hidelab/pc
>> xn.git>
>> > (push)upstream git at git.bioconductor.org:packages/pcxn.git
>> > (fetch)upstream git at git.bioconductor.org:packages/pcxn.git
>> (push)*
>> > The ssh command also gives:
>> >
>> >
>> >
>> >
>> > *Warning: Permanently added 'git.bioconductor.org
>> > <http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of
>> known
>> > hosts.Permission denied (publickey).*
>> >
>> > *Cheers,*
>> >
>> > *Sokratis*
>> >
>> >
>> > On 23 March 2018 at 11:35, Shepherd, Lori <
>> Lori.Shepherd at roswellpark.org>
>> > wrote:
>> >
>> >> Where you able to update master? Or are you having access trouble
>> >> for both branches? Please use reply all so that other members on the
>> team
>> >> can answer when appropriate and the responses go to the mailing list.
>> >>
>> >> Your package is in the git repository and has access with the ID
>> s.kariotis.
>> >> Can you please copy the commands with the output you are receiving that
>> >> make you think that you do not have access?
>> >>
>> >> Please also include the output of
>> >>
>> >> git remote -v
>> >>
>> >> and
>> >>
>> >> ssh -T git at git.bioconductor.org
>> >> (you should see RW access next to your package)
>> >>
>> >>
>> >> Please
>> >>
>> >>
>> >>
>> >> Lori Shepherd
>> >>
>> >> Bioconductor Core Team
>> >>
>> >> Roswell Park Cancer Institute
>> >>
>> >> Department of Biostatistics & Bioinformatics
>> >>
>> >> Elm & Carlton Streets
>> >>
>> >> Buffalo, New York 14263
>> >>
>> >>
>> >> ------------------------------
>> >> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
>> >> Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
>> >> *Sent:* Friday, November 24, 2017 10:13 AM
>> >> *To:* Sokratis Kariotis; bioc-devel
>> >> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>> >>
>> >> You should make changes and push to the master branch of your package
>> at
>> >> git at git.bioconductor.org:packages/pcxnData.git . This will update
>> the
>> >> devel version of your package.
>> >>
>> >> As long as the package builds correctly, It will be available for
>> download
>> >> immediately with Bioc devel 3.7.
>> >>
>> >>
>> >> We don't encourage updating release unless it is a bug correction or
>> >> justifiable updates, but if you push changes to the RELEASE_3_6 branch
>> they
>> >> will also be available in Bioc 3.6
>> >>
>> >>
>> >> Instructions for pushing data to our git repository can be found here:
>> >>
>> >> http://bioconductor.org/developers/how-to/git/
>> >>
>> >>
>> >> Remember to do a pull from our git repositories if you have not done so
>> >> since the release as we update the versions when rolling out the
>> release.
>> >>
>> >> http://bioconductor.org/developers/how-to/version-numbering/
>> >>
>> >>
>> >>
>> >> Lori Shepherd
>> >>
>> >> Bioconductor Core Team
>> >>
>> >> Roswell Park Cancer Institute
>> >>
>> >> Department of Biostatistics & Bioinformatics
>> >>
>> >> Elm & Carlton Streets
>> >>
>> >> Buffalo, New York 14263
>> >>
>> >> ________________________________
>> >> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
>> Sokratis
>> >> Kariotis <s.kariotis at sheffield.ac.uk>
>> >> Sent: Friday, November 24, 2017 10:02:13 AM
>> >> To: bioc-devel
>> >> Subject: [Bioc-devel] Update data in data package, pcxnData
>> >>
>> >> Hi all,
>> >>
>> >> I have a data package (pcxnData) that got released in 3.6 and I am
>> >> wondering how long will it take, if I changed some of the data in that
>> >> package for them to be publicly available in bioconductor instead of
>> the
>> >> old data. Can they be available sooner than the next release? Thanks in
>> >> advance.
>> >>
>> >> Cheers,
>> >> Sokratis Kariotis
>> >>
>> >>
>> >>
>> >> --
>> >> Sokratis Kariotis
>> >> Scientific Programmer
>> >> Hidelab
>> >> Sheffield Institute for Translational Neuroscience
>> >> 385a Glossop Rd, Sheffield, S10 2HQ
>> >> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+
>> 2HQ&entry=gmail&source=g>
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
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>> >
>> >
>> >
>> > --
>> > Sokratis Kariotis
>> > Scientific Programmer
>> > Hidelab
>> > Sheffield Institute for Translational Neuroscience
>> > 385a Glossop Rd, Sheffield, S10 2HQ
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
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>>
>
>
>
> --
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
>
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
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