Re: [Bioc-devel] Update data in data package, pcxnData
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 B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp > +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0 > Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL > xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZ > j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW > cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvs
Re: [Bioc-devel] Update data in data package, pcxnData
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<mailto: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<mailto: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<mailto: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<mailto:nitesh.tur...@roswellpark.org>> wrote: Hi Sokratis, Your key(s) on file is ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/
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 B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp > +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0 > Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL > xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZ > j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW > cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB > > ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+Q > V5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6n > FfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+ > rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80T > a0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJ > Yw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd > > ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkB > CHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2 > CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0 > UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR > 2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8 > cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf > > s
Re: [Bioc-devel] Update data in data package, pcxnData
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<mailto: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<mailto:nitesh.tur...@roswellpark.org>> wrote: Hi Sokratis, Your key(s) on file is ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf ssh-rsa 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 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 Ma
Re: [Bioc-devel] Update data in data package, pcxnData
>> > >> > >> > >> > >> > *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 >> >> >> >> >> >> >> >> -- >> >> S
Re: [Bioc-devel] Update data in data package, pcxnData
-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=gmail=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 > > > > [[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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Update data in data package, pcxnData
Hi Sokratis, Your key(s) on file is ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf ssh-rsa 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 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)upstreamg...@git.bioconductor.org:packages/pcxn.git > (fetch)upstreamg...@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/
Re: [Bioc-devel] Update data in data package, pcxnData
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)upstreamg...@git.bioconductor.org:packages/pcxn.git (fetch)upstreamg...@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=gmail=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 h
Re: [Bioc-devel] Update data in data package, pcxnData
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 [[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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
