Everything seems to be fine and the 3_6 release is online. Thanks for the help!
Cheers, Sokratis On 5 April 2018 at 18:41, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > We are taking care of this on our end. Sorry for the confusion. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk> > *Sent:* Thursday, April 5, 2018 8:02:14 AM > *To:* Shepherd, Lori > *Cc:* Turaga, Nitesh; bioc-devel > > *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData > > 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.sheph...@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.kario...@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.kario...@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.tur...@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.kario...@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 g...@git.bioconductor.org:packages/pcxn.git > > (fetch)upstream g...@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.sheph...@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 g...@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-boun...@r-project.org> on behalf of > >> Shepherd, Lori <lori.sheph...@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 > >> g...@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-boun...@r-project.org> on behalf of > Sokratis > >> Kariotis <s.kario...@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@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. > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@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> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@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 > <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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
