[Bioc-devel] Update data in data package, pcxnData

Thu Apr 5 14:02:14 CEST 2018

Hey all,

The issues remain the same in both packages:

https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/malbec1-buildsrc.html

https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html

Regards,
Sokratis

On 30 March 2018 at 18:53, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
wrote:

> I believe this should clear up in a few days.  Because of the circular
> dependencies, it will require a few passes through the build system.
>
>
> For example:
>
>
> First pass:
>
> The pcxnData package has a force install, so it will get installed even
> if it fails the build and check. The pcxn package will also fail its first
> pass through.
>
>
> Second pass:
>
> the pcxn package will find the newly installed version of the pcxnData
> package and pass.  The pcxnData package will still fail
>
>
> Third pass:
>
> pcxnData will find the newly built software package and pass as will the
> linux version of the software package.
>
>
> Forth pass:
>
> May be needed for the mac and windows versions to find the new data
> package.
>
>
>
> The last update to the software package was on March 27 - which probably
> missed being pulled for the March 28th report so probably included for the
> March 29th build report
>
> March 29th  - both fail (but there was a force install behind the scenes)
>
> March 30th -  data package fails, but the linux version of the software
> package built and propagated
>
> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> pcxn/malbec1-buildsrc.html
>
>
> My guess is that by Sunday's or Monday's build reports everything will be
> okay.
>
> I will keep an eye on this to make sure its the case and please let us
> know if you still are seeing issues next week.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
> *Sent:* Thursday, March 29, 2018 6:49:47 AM
> *To:* Turaga, Nitesh
> *Cc:* Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> 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.html , 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+mRcD7dJyFt1CySEbxVZ
> j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW
> cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB
>
> 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/p89lvljsvlE7vbxdqFmeobGSQ
> 6ftDq5btdEHfD2rc++iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9s
> BL5gLFHTkl3KyxNdIsH9j0iNFdJmEHySZh2ePdrqG7ZE/FOKf77XTX+acqgy
> dF+Dsep16lTIxk94MXLk7Sz2v8XQqFtETa5q0Gkm70Ok/qht/O80nWUT3QX4
> 4sPM4ivPckOHwnZjywpZyBONas26hP0M1pZSEvB5qLCMKyD4YmTJ5aZkeCHh
> 6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ==
>
> 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/pcxn.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>
> >> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+
> 2HQ&entry=gmail&source=g>
> >>
> >>        [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
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> or
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
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> >> agent responsible for the delivery of this message to the intended
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> >
> >
> >
> > --
> > 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]]
> >
> > _______________________________________________
> > 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
> e-mail and delete this email message from your computer. Thank you.
>
>
>
>
> --
> 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>
>
>
>
>
> --
> 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>
>
> 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
> e-mail and delete this email message from your computer. Thank you.
>

-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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