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

3 messages · Shepherd, Lori, Sokratis Kariotis

Original

1

3

Sokratis Kariotis

Thu, Apr 5, 2018 5:02 AM #

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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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.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

_______________________________________________
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

_______________________________________________
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

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

	[[alternative HTML version deleted]]

Thu, Apr 5, 2018 10:41 AM #

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.kariotis at 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.Shepherd at roswellpark.org<mailto: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<mailto: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<mailto: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<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
Hi Sokratis,

Your key(s) on file is

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC7QB8rwK1n7/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.kariotis at sheffield.ac.uk<mailto: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>
> <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>
> <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<mailto: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<mailto: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<mailto: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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Sokratis
>> Kariotis <s.kariotis at sheffield.ac.uk<mailto: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<mailto: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
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> Sheffield Institute for Translational Neuroscience
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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>

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


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.

4 days later

Sokratis Kariotis

Tue, Apr 10, 2018 4:50 AM #

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.Shepherd at 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.kariotis at 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.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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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.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

_______________________________________________
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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

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