[Bioc-devel] Can't push to RadioGx upstream

[Chris Eeles]

Hello BioC core team,

I am unable to push to the RadioGx upstream master, despite being able to push 
to CoreGx, PharmacoGx and ToxicoGx.

The error is:
ceeles@EELESPC-Desk:~/Development/RadioGx$ git push upstream master
FATAL: W any packages/RadioGx b.haibe-kains DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

You can see my remotes here:
ceeles@EELESPC-Desk:~/Development/RadioGx$ git remote -v
origin  g...@github.com:bhklab/RadioGx.git (fetch)
origin  g...@github.com:bhklab/RadioGx.git (push)
upstreamg...@git.bioconductor.org:packages/RadioGx.git (fetch)
upstreamg...@git.bioconductor.org:packages/RadioGx.git (push)

I also double checked my SSH key is configured in Bioc Git Credential manager.

I am also unable to login to Bioconductor Git Credentials using my personal 
email (christopher.ee...@outlook.com), but can do so using Benjamins email 
(benjamin.haibe.ka...@utoronto.ca).

I tried resetting my password but did not receive an email. I should have 
access to the credential manager via my own email.

Assistance with this would be appreciated.

Best,
Christopher Eeles
Software Developer
BHK Lab | PM-Research | UHN

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[Bioc-devel] No write permissions on PDATK

[Chris Eeles]

Hello Core Team,

I am trying to push a fix for our package, PDATK, to Bioconductor but it seems 
I have lost write permissions on the repo, as indicated by `ssh -T 
g...@git.bioconductor.org | grep PDATK`. I 
also tried to login to the BiocCredentials app, but it seems the password has 
changed and I do not receive an email when I try to reset it.

Any help would be appreciated. My SSH key grants access to all other package we 
maintain.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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Re: [Bioc-devel] Best Practices for Renaming S4 Slots

[Chris Eeles]

Hi Vincent,

Thanks for sharing your thoughts.

I guess my thinking was that the entire point of using S4 classes and OOP is 
having accessor methods to provide an implementation independent API. In the 
Bioconductor guidelines it specifically tells users not to access slots using 
the `@` operator, as an implementation change in the class may break any 
scripts doing so. Therefore, my changing slot names should have no effect on 
users following the Bioconductor coding best practices, assuming I maintain the 
old accessors methods with a .Deprecation warning, as per the cited guideline. 
That was indeed my plan.

So I would argue that no, class definitions are not part of the API, especially 
if I am just renaming slots. Indeed isn't that one of the supposed strengths of 
OOP programming and the use of interfaces?

Obviously I have already agreed to wait for 3.15 to make the changes, but I do 
not think it is clear from the current guidelines that deprecation rules apply 
to slots. Given that `@` isn't even a generic, there would be no way to send a 
message to the user except through the accessor methods, which they would never 
see if they weren't already using the accessor API. So for users accessing data 
via `@`, the deprecation guidelines provide no benefits because they failed to 
follow the best practices.

My opinion of the developer-user contract for S4 classes is that the API would 
not change without due warning, and if implementation really is independent of 
interface, then any changes made to an S4 class should be fine, so long as all 
the original methods still work and can be deprecated according to the cited 
guidelines.

Additionally, if changes to a class require so much work, it incentives 
developers to simply ditch old S4 classes and reimplement them in a new 
package. Doesn't that go against the spirit of reuse that is supposed to be 
encouraged by adoption of S4 classes?

TL;DR - IMO API = interface; implementation is developer business

Best,
Chris

From: Vincent Carey 
Sent: October 15, 2021 1:31 PM
To: Chris Eeles 
Cc: Herv� Pag�s ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

I will defer to Herve about all details, but I would say that this level of 
change control is implied by the "no changes
to package API without an interval of deprecation spanning at least one 
release".  See 
https://bioconductor.org/developers/how-to/deprecation/<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fdeprecation%2F=04%7C01%7C%7C8ec56a4ffda74802e7ab08d990019bc7%7C84df9e7fe9f640afb435%7C1%7C0%7C637699158846578705%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000=1vILqDKSUJPMJ5gKZ1y%2Ftlf8rKtrZmX6tL6xGTINEo8%3D=0>
That text mentions that removal may take 18 months.

Whatever is exposed cannot be changed without a deprecation period,
in which the functionality is preserved, but notification is given to 
users/developers, through .Deprecated, that
functionality will change and advice is given on the alternate approach to be 
used.

Is a slot name part of the API?  It isn't completely obvious, but in the case 
of serialized objects, it turns out that it is.
I don't know that our guidelines have sufficient details on this process, but 
we welcome your input on where to
best outline/advertise this.

On Fri, Oct 15, 2021 at 1:22 PM Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:
Message received. I will leave that branch for later. Is this information 
available on the Bioconductor website at all? It would have been useful to find 
out sooner.

Best,
Chris

-Original Message-
From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> On 
Behalf Of Chris Eeles
Sent: October 15, 2021 1:10 PM
To: Herv� Pag�s 
mailto:hpages.on.git...@gmail.com>>; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Thanks Herve,

I actually got the updateObject method working after sending this email, but 
thanks for the information. Maybe it is worth adding a section on this topic to 
the Bioconductor developer section?

Unfortunately, I was unaware that the start of development cycle was the best 
time to implement this change. I am currently planning to have this done for 
the 3.14 release.

I am introducing new accessors as well but keeping the old ones for backwards 
compatibility using aliases.

How discouraged are slot name changes in a release? A lot of the changes on our 
road map require the slots to be renamed so it would significantly delay 
required features if I were to wait.

I plan to put in the work so that those using accessors shouldn't notice a 
difference.

Best,
Chris

-Original Message-
From: Herv� Pag�s 
mailto:hpages.on.git...@gmail.com>>
Sent: October 15, 2021 12:39 PM
To: Chris Eeles 
mailto:

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

[Chris Eeles]

Message received. I will leave that branch for later. Is this information 
available on the Bioconductor website at all? It would have been useful to find 
out sooner.

Best,
Chris

-Original Message-
From: Bioc-devel  On Behalf Of Chris Eeles
Sent: October 15, 2021 1:10 PM
To: Hervé Pagès ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Thanks Herve,

I actually got the updateObject method working after sending this email, but 
thanks for the information. Maybe it is worth adding a section on this topic to 
the Bioconductor developer section?

Unfortunately, I was unaware that the start of development cycle was the best 
time to implement this change. I am currently planning to have this done for 
the 3.14 release.

I am introducing new accessors as well but keeping the old ones for backwards 
compatibility using aliases.

How discouraged are slot name changes in a release? A lot of the changes on our 
road map require the slots to be renamed so it would significantly delay 
required features if I were to wait.

I plan to put in the work so that those using accessors shouldn't notice a 
difference.

Best,
Chris

-Original Message-
From: Hervé Pagès 
Sent: October 15, 2021 12:39 PM
To: Chris Eeles ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Hi Chris,

There was some formatting issues with my previous answer so I'm sending it 
again. Hopefully this time the formatting is better. See below.

On 14/10/2021 13:08, Chris Eeles wrote:
> Hello BioC community,
> 
> I am the lead developer for the CoreGx, PharmacoGx, RadioGx and ToxicoGx 
> packages. We have recently been working on major updates to the structure of 
> a CoreSet, which is inherited by the main class in all three of the other 
> packages listed.
> 
> While making these changes, we would like to rename some CoreSet slots to 
> increase the amount of code that can be refactored into CoreGx, simplifying 
> maintenance and development of inheriting packages in the future.
> 
> The slot names and their accessors will be made more generic, for example the 
> 'cell' slot will become 'sample' to allow a CoreSet derived class to store 
> Biological model systems other than cancer cell lines. Similarly, 'drug' or 
> 'radiation' slots in inheriting packages will be replaced with a 'treatment' 
> slot in the CoreSet. This will allow us to simplify inheritance, removing 
> much redundant code from the inheriting packages and setting us up to 
> integrate other lab packages, such as Xeva for PDX models, into the general 
> CoreSet infrastructure.
> 
> I took a brief look through the Bioconductor developer documentation but 
> didn't see anything talking about best practices for renaming slots.
> 
> It is easy enough to make the code changes, but my major concern is being 
> able to update existing objects from these packages to use the new slot names.
> 
> I am aware of the updateObject function in BiocGenerics, but tried using it 
> to update some example data in CoreGx without success.
> 
> Is this the proper function to use when you wish to update an S4 object whose 
> class definition has been modified? If not, is there existing infrastructure 
> for accomplishing this task?

Yes updateObject() is the proper function to use but the function has no way to 
guess how to fix your objects. The way you tell it what to do is by 
implementing methods for your objects.

For example if you renamed the 'cell' slot -> 'sample', your
updateObject() method will be something like this:


setMethod("updateObject", "CoreSet",
 function(object, ..., verbose=FALSE)
 {
 ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
 if (.hasSlot(object, "cell")) {
 object <- new("CoreSet",
   sensitivity=object@sensitivity,
   annotation=object@annotation,
   molecularProfiles=object@molecularProfiles,
   sample=object@cell,
   datasetType=object@datasetType,
   perturbation=object@perturbation,
   curation=object@curation)
 return(object)
 }
 object
 }
)

The best time to do this internal renaming is at the beginning of the BioC 3.15 
development cycle (i.e. right after the 3.14 release).

If in the future, other slots get renamed or added, you'll need to modify the 
updateObject() method above like this:

setMethod("updateObject", "CoreSet",
 function(object, ..., verbose=FALSE)
 {
 ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
 if (.hasSlot(object, "cell")) {
 

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

[Chris Eeles]

Thanks Herve,

I actually got the updateObject method working after sending this email, but 
thanks for the information. Maybe it is worth adding a section on this topic to 
the Bioconductor developer section?

Unfortunately, I was unaware that the start of development cycle was the best 
time to implement this change. I am currently planning to have this done for 
the 3.14 release.

I am introducing new accessors as well but keeping the old ones for backwards 
compatibility using aliases.

How discouraged are slot name changes in a release? A lot of the changes on our 
road map require the slots to be renamed so it would significantly delay 
required features if I were to wait.

I plan to put in the work so that those using accessors shouldn't notice a 
difference.

Best,
Chris

-Original Message-
From: Hervé Pagès  
Sent: October 15, 2021 12:39 PM
To: Chris Eeles ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Hi Chris,

There was some formatting issues with my previous answer so I'm sending it 
again. Hopefully this time the formatting is better. See below.

On 14/10/2021 13:08, Chris Eeles wrote:
> Hello BioC community,
> 
> I am the lead developer for the CoreGx, PharmacoGx, RadioGx and ToxicoGx 
> packages. We have recently been working on major updates to the structure of 
> a CoreSet, which is inherited by the main class in all three of the other 
> packages listed.
> 
> While making these changes, we would like to rename some CoreSet slots to 
> increase the amount of code that can be refactored into CoreGx, simplifying 
> maintenance and development of inheriting packages in the future.
> 
> The slot names and their accessors will be made more generic, for example the 
> 'cell' slot will become 'sample' to allow a CoreSet derived class to store 
> Biological model systems other than cancer cell lines. Similarly, 'drug' or 
> 'radiation' slots in inheriting packages will be replaced with a 'treatment' 
> slot in the CoreSet. This will allow us to simplify inheritance, removing 
> much redundant code from the inheriting packages and setting us up to 
> integrate other lab packages, such as Xeva for PDX models, into the general 
> CoreSet infrastructure.
> 
> I took a brief look through the Bioconductor developer documentation but 
> didn't see anything talking about best practices for renaming slots.
> 
> It is easy enough to make the code changes, but my major concern is being 
> able to update existing objects from these packages to use the new slot names.
> 
> I am aware of the updateObject function in BiocGenerics, but tried using it 
> to update some example data in CoreGx without success.
> 
> Is this the proper function to use when you wish to update an S4 object whose 
> class definition has been modified? If not, is there existing infrastructure 
> for accomplishing this task?

Yes updateObject() is the proper function to use but the function has no way to 
guess how to fix your objects. The way you tell it what to do is by 
implementing methods for your objects.

For example if you renamed the 'cell' slot -> 'sample', your
updateObject() method will be something like this:


setMethod("updateObject", "CoreSet",
 function(object, ..., verbose=FALSE)
 {
 ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
 if (.hasSlot(object, "cell")) {
 object <- new("CoreSet",
   sensitivity=object@sensitivity,
   annotation=object@annotation,
   molecularProfiles=object@molecularProfiles,
   sample=object@cell,
   datasetType=object@datasetType,
   perturbation=object@perturbation,
   curation=object@curation)
 return(object)
 }
 object
 }
)

The best time to do this internal renaming is at the beginning of the 
BioC 3.15 development cycle (i.e. right after the 3.14 release).

If in the future, other slots get renamed or added, you'll need to 
modify the updateObject() method above like this:

setMethod("updateObject", "CoreSet",
 function(object, ..., verbose=FALSE)
 {
 ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
 if (.hasSlot(object, "cell")) {
 object <- new("CoreSet",
   sensitivity=object@sensitivity,
   annotation=object@annotation,
   molecularProfiles=object@molecularProfiles,
   sample=object@cell,
   datasetType=object@datasetType,
   perturbation=object@perturbation,

[Bioc-devel] Best Practices for Renaming S4 Slots

[Chris Eeles]

Hello BioC community,

I am the lead developer for the CoreGx, PharmacoGx, RadioGx and ToxicoGx 
packages. We have recently been working on major updates to the structure of a 
CoreSet, which is inherited by the main class in all three of the other 
packages listed.

While making these changes, we would like to rename some CoreSet slots to 
increase the amount of code that can be refactored into CoreGx, simplifying 
maintenance and development of inheriting packages in the future.

The slot names and their accessors will be made more generic, for example the 
'cell' slot will become 'sample' to allow a CoreSet derived class to store 
Biological model systems other than cancer cell lines. Similarly, 'drug' or 
'radiation' slots in inheriting packages will be replaced with a 'treatment' 
slot in the CoreSet. This will allow us to simplify inheritance, removing much 
redundant code from the inheriting packages and setting us up to integrate 
other lab packages, such as Xeva for PDX models, into the general CoreSet 
infrastructure.

I took a brief look through the Bioconductor developer documentation but didn't 
see anything talking about best practices for renaming slots.

It is easy enough to make the code changes, but my major concern is being able 
to update existing objects from these packages to use the new slot names.

I am aware of the updateObject function in BiocGenerics, but tried using it to 
update some example data in CoreGx without success.

Is this the proper function to use when you wish to update an S4 object whose 
class definition has been modified? If not, is there existing infrastructure 
for accomplishing this task?

Any tips for implementing slot renaming, as well as links to existing 
documentation or articles on the topic would be appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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[Bioc-devel] Can't push to upstream for ToxicoGx

[Chris Eeles]

Hello BioC core team,

I am having a weird issue with pushing a fix to the ToxicoGx repo. I tried 
removing and re-adding the upstream branch, but the problem still persists.

I can fetch and pull from the remote using my SSH key, I can also access our 
CoreGx repo (push and pull) using the same key.

However, when I try to push to upstream master I get this error:
(py39) ceeles@EELESPC-DESK:~/development/ToxicoGx$ git push upstream master
Enter passphrase for key '/home/ceeles/.ssh/bioc_rsa':
FATAL: W any packages/ToxicoGx b.haibe-kains DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

This is the same SSH key I have been using for years and I have pushed to this 
repository in the past without issue.

Not sure what has gone wrong, some help would be appreciated as there is 
currently and ERROR in the development branch.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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[Bioc-devel] Bioconductor 3.14 R Version

[Chris Eeles]

Hello Bioc Core Team,

I noticed that currently Bioconductor 3.14 is building using R 4.1.0 beta. Will 
this be changed to R 4.2 in the future?

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory
Princess Margaret Cancer 
Centre
University Health 
Network


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Re: [Bioc-devel] 3.12 builds

[Chris Eeles]

Hi Herve,

Can you clarify what you mean by after tomorrow? The deadline is Friday, 
October 23rd correct? Is there a time of day submissions need to be made by?

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network


-Original Message-
From: Bioc-devel  On Behalf Of Pages, Herve
Sent: October 21, 2020 12:47 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] 3.12 builds

Hi developers,

Sorry that we didn't have an updated report yesterday (Tuesday October
20) for the BioC 3.12 builds. The new report for today is out:

   
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fdata=04%7C01%7C%7Cdb74d3dcc1ee4450152808d875e0f451%7C84df9e7fe9f640afb435%7C1%7C0%7C637388956316409640%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=aqxLcJlJIheHZAWesVsn9uG%2F4UkRUxjlM4XbjT%2F6RMs%3Dreserved=0

Please address any remaining issue with your packages as soon as possible. Only 
two days left! The deadline for packages passing 'R CMD build' and 'R CMD 
check' without errors or warnings is after tomorrow (Friday October 23).

Thanks for your contribution to the project.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Changing Package Maintainer

[Chris Eeles]

Hi Nitesh,

Thanks for getting back to me. So in the future to change maintainers I can 
simply update the DESCRIPTION?

I wasn’t sure based on the issues we had with the credentials account and 
didn’t want to assume.

Best,
Chris

From: Nitesh Turaga 
Sent: July 8, 2020 8:13 AM
To: Chris Eeles ; Haibe-Kains, Benjamin 

Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Changing Package Maintainer

Hi Chris,

The email 
benjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca> is 
registered to you Chris Eeles.

You should be added to the packages now for access. However the “maintainer” 
field in the description file needs to be changed by you.

Best,

Nitesh


On Jul 6, 2020, at 12:42 PM, Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:

Hello Bioconductor developers,

Michael and I would like to change the package maintainer for the 
MetaGxPancreas and MetaGxBreast data packages from Michael to: Benjamin 
Haibe-Kains 
mailto:benjamin.haibe.ka...@utoronto.ca>>

If someone could assist me with this it would be greatly appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory<http://www.bhklab.ca/<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7C%7C3fecb598933d4b25030108d823384a21%7C84df9e7fe9f640afb435%7C1%7C0%7C637298072145536844=V9UClJtNZnUqTrIcqA25xP3MjFXuGj4nMgzLWUsP1xY%3D=0>>
Princess Margaret Cancer 
Centre<https://www.pmgenomics.ca/pmgenomics/<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7C%7C3fecb598933d4b25030108d823384a21%7C84df9e7fe9f640afb435%7C1%7C0%7C637298072145536844=%2F8t4hdY9DNKTC9xpCMwtfkmn0VKjQLOiPeOZBHh58wE%3D=0>>
University Health 
Network<http://www.uhn.ca/<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F=02%7C01%7C%7C3fecb598933d4b25030108d823384a21%7C84df9e7fe9f640afb435%7C1%7C0%7C637298072145546836=95S%2BbGT%2FNEUWmMO9%2FJ9LjgI%2BO0TUvw8ubYwqAj0%2B9MM%3D=0>>



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[Bioc-devel] Changing Package Maintainer

[Chris Eeles]

Hello Bioconductor developers,

Michael and I would like to change the package maintainer for the 
MetaGxPancreas and MetaGxBreast data packages from Michael to: Benjamin 
Haibe-Kains 

If someone could assist me with this it would be greatly appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network



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Re: [Bioc-devel] Bioconductor credentials issue

[Chris Eeles]

Hi Nitesh,

I had to reset the password but yes I can.

Best,
Chris

From: Nitesh Turaga 
Sent: Friday, June 19, 2020 10:40:41 AM
To: Chris Eeles 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Bioconductor credentials issue

Hi Chris,

Let�s try it this way.

It seems that the maintainer listed on all the packages is with the email 
�benjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca>�. 
I�m guessing you have access to this email address, i.e see the emails which go 
this address (or are forwarded to you by Ben). Right now, the way this email is 
configured is, it has your Github and SSH keys with it.

I guess the first question is, are you able to log in to the BiocCredentials 
account?

Nitesh

On Jun 18, 2020, at 10:51 AM, Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:

Hi Nitesh,

The only thing I can think of is that I opened my package submission issues 
under my GitHub account, but listed the maintainer as my PI, Benjamin 
Haibe-Kains. Is this something the system normally deals with  (a developer 
submitting on behalf of a PI)? Maybe the maintainer 
(benjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca>) 
credentials account is getting updated with my user name on package acceptance?

I can image if this is the case that my credentials account 
(christopher.ee...@outlook.com<mailto:christopher.ee...@outlook.com>) may get 
disabled due to a duplicate GitHub username/ID? Access to the accounts was only 
lost after the recent acceptance of RadioGx and ToxicoGx.

This is all speculation, but package submission/acceptance is the only action I 
have taken since I was able to successfully login with both accounts and push 
using my SSH key.

Otherwise, maybe the credentials DB got rolled back? Not really sure what else 
would cause this.

If you can resolve the issue again this would be appreciated. Our packages are:
consensusOV
CoreGx
genefu
PharmacoGx
predictionnet
RadioGx
survcomp
ToxicoGx
Xeva

If you think duplicated account public keys may be the cause, could you 
reinitialize my credentials account without any SSH keys and I will add a 
different one?

Thanks for your assistance.

Best,
Chris


From: Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Sent: June 18, 2020 8:46 AM
To: Chris Eeles 
mailto:christopher.ee...@outlook.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Bioconductor credentials issue

Hi Chris,

This is a very strange problem which I haven�t come across before. But let me 
say this though, the fact that this email 
"benjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca>� is 
connected to your username, Github ID and has your SSH keys is not correct.

I fixed this last time by making you an account and giving you access through 
an account registered 
tochristopher.ee...@outlook.com<mailto:christopher.ee...@outlook.com>. I�m not 
sure what happened there? Any insight?

Nitesh



On Jun 17, 2020, at 10:51 AM, Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:

Hello Bioconductor team,

I am having issues accessing our labs Bioconductor repositories and also cannot 
login to the Bioconductor credentials website.

I had a similar issue less than a month ago, which Nitesh from the core team 
helped me resolve. At that time I was able to login to Bioconductor credentials 
for 
bothbenjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca><mailto:benjamin.haibe.ka...@utoronto.ca>
 (my PI's maintainer email) as well as 
christopher.ee...@outlook.com<mailto:christopher.ee...@outlook.com><mailto:christopher.ee...@outlook.com>
 (my GitHub account) and could push to upstream for all my packages. I can no 
longer do any of those things and do not get an email when I attempt to reset 
the password on the credentials account 
forchristopher.ee...@outlook.com<mailto:christopher.ee...@outlook.com><mailto:christopher.ee...@outlook.com>.

Recently, two of my package submissions (RadioGx, ToxicoGx) were accepted. This 
is the only change I can think of which may be the source of the issue.

If someone could advise on how to resolve this issue, it would be appreciated.

I have updates I am waiting to push to RadioGx.

Thanks for your assistance.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory<http://www.bhklab.ca/<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7C%7C83297c76e0bc42b28bb208d8145ebf0a%7C84df9e7fe9f640afb435%7C1%7C0%7C637281744644051728=g6I%2FoG6Yjg365k5QngIn8vMaex6SkCP6UsCxAiVTArA%3D=0>>
Princess Margaret Cancer 
Centre<https://www.pmgenomics.ca/pmgenomics/<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7C%7C83297c76e0bc42b28bb208d8145ebf0a%7C84df9e7fe9f64

[Bioc-devel] Bioconductor credentials issue

[Chris Eeles]

Hello Bioconductor team,

I am having issues accessing our labs Bioconductor repositories and also cannot 
login to the Bioconductor credentials website.

I had a similar issue less than a month ago, which Nitesh from the core team 
helped me resolve. At that time I was able to login to Bioconductor credentials 
for both 
benjamin.haibe.ka...@utoronto.ca (my 
PI's maintainer email) as well as 
christopher.ee...@outlook.com (my GitHub 
account) and could push to upstream for all my packages. I can no longer do any 
of those things and do not get an email when I attempt to reset the password on 
the credentials account for 
christopher.ee...@outlook.com.

Recently, two of my package submissions (RadioGx, ToxicoGx) were accepted. This 
is the only change I can think of which may be the source of the issue.

If someone could advise on how to resolve this issue, it would be appreciated.

I have updates I am waiting to push to RadioGx.

Thanks for your assistance.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network







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Re: [Bioc-devel] SSH Issues

[Chris Eeles]

Hi Nitesh,

I did not change the username on purpose, maybe it happened because I submitted 
CoreGx under my GitHub account with Benjamin listed as the maintainer?

Anyway, all of our package on Bioconductor are:

  *   genefu
  *   PharmacoGx
  *   predictionnet
  *   survcomp
  *   Xeva
  *   consensusOV
  *   CoreGx

Benjamin’s GitHub username is bhaibeka, if I just change the username back will 
that work?

Sorry for an inconvenience.

Best,
Chris

From: Nitesh Turaga 
Sent: June 3, 2020 1:15 PM
To: Chris Eeles 
Cc: bioc-devel@r-project.org; Haibe-Kains, Benjamin 

Subject: Re: [Bioc-devel] SSH Issues

Hi Chris,

I just checked and it seems you have changed the username in Benjamin’s 
account. Is that correct?

So, the mapping is lost for all the packages Benjamin had, and your username as 
well has lost all of it’s mapping on Git repo.

Can you tell me what packages you need access to? We should keep Benjamin’s 
account at his 
‘utoronto.ca<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Futoronto.ca%2F=02%7C01%7C%7C27cb7946457d4b13907108d807e1a694%7C84df9e7fe9f640afb435%7C1%7C0%7C637268013222071484=oy5bAg2L8ZyLGTYEhLoVRV0iH8Oto3iCnTtsdVEEZR4%3D=0>’
 separate from yours.

I’ll create an account for you and give you access. I’ll have to fix benjamin’s 
account and yours as well/

Best,

Nitesh



On Jun 3, 2020, at 12:56 PM, Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:

Hi Nitesh,

I had a look at the packages I have access to and it seems that the 
Bioconductor credentials account I logged into only has access to the Xeva 
repo. I am using 
‘benjamin.haibe.ka...@utoronto.ca<mailto:benjamin.haibe.ka...@utoronto.ca>', 
the email listed as maintainer for all of the BHKLAB Bioconductor submissions.


Which email would the credentials be managed if not the maintainers’?

I tried activating an account using my GitHub email but it says I am not the 
maintainer of any packages.

Are you able to see which email the credentials for PharmacoGx and CoreGx are 
managed under? If not how can I manage access to these repos?

Thanks for your support.

Best,
Chris

From: Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Sent: June 3, 2020 11:05 AM
To: Chris Eeles 
mailto:christopher.ee...@outlook.com>>
Cc: Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] SSH Issues

Hi Chris,

http://bioconductor.org/developers/how-to/git/faq/<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Ffaq%2F=02%7C01%7C%7C27cb7946457d4b13907108d807e1a694%7C84df9e7fe9f640afb435%7C1%7C0%7C637268013222071484=A7Zxee0BmsukYqKMoaueyryPUre%2F4j6yqZW4ermkaNo%3D=0>
 Take a look at #13 and #14.

I’ll be able to better help you with more information.

Best,

Nitesh



On Jun 3, 2020, at 10:49 AM, Chris Eeles 
mailto:christopher.ee...@outlook.com>> wrote:

Hello Bioconductor team,

I am having issues pushing updates to the development branch of the CoreGx 
package.

When I try to push to upstream I get:
"FATAL: W any packages/CoreGx gangeshberiuhn DENIED by fallthru
(or you mis-spelled the reponame)
Fatal: Could not read from remote repository.

Please make sure you have the correct access rights
on the repository and the repository exists."

I have access to our Bioconductor credentials account and have confirmed that 
my public key is registered there, so I am not sure what is going on. I also 
tried removing and re-adding upstream.

Any help would be appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK 
Laboratory<http://www.bhklab.ca/<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7C%7C27cb7946457d4b13907108d807e1a694%7C84df9e7fe9f640afb435%7C1%7C0%7C637268013222081479=JFmkXRxuxJJG1FE%2F0N8Gxq96ocipbuhF1gg0vTw42ic%3D=0>>
Princess Margaret Cancer 
Centre<https://www.pmgenomics.ca/pmgenomics/<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7C%7C27cb7946457d4b13907108d807e1a694%7C84df9e7fe9f640afb435%7C1%7C0%7C637268013222081479=LnvKW%2Bl38rc88zsHldvPPPnkDmqOLvlp9fAiG0PWRRQ%3D=0>>
University Health 
Network<http://www.uhn.ca/<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F=02%7C01%7C%7C27cb7946457d4b13907108d807e1a694%7C84df9e7fe9f640afb435%7C1%7C0%7C637268013222081479=08gO6fz73rMPzceX0dlITunPHbeZnz8LsTzyQKCVToc%3D=0>>




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[Bioc-devel] SSH Issues

[Chris Eeles]

Hello Bioconductor team,

I am having issues pushing updates to the development branch of the CoreGx 
package.

When I try to push to upstream I get:
"FATAL: W any packages/CoreGx gangeshberiuhn DENIED by fallthru
(or you mis-spelled the reponame)
Fatal: Could not read from remote repository.

Please make sure you have the correct access rights
on the repository and the repository exists."

I have access to our Bioconductor credentials account and have confirmed that 
my public key is registered there, so I am not sure what is going on. I also 
tried removing and re-adding upstream.

Any help would be appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network




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[Bioc-devel] Package Submission Limbo

[Chris Eeles]

Hello Bioconductor team and community,

My name is Christopher Eeles and I am a software developer in the Benjamin 
Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, 
Ontario, Canada.

I am concerned due to inaction on the part of my reviewer for two of my package 
submissions, and am not sure how to move forward.

Initially, I submitted three packages - CoreGx, ToxicoGx and RadioGx - on April 
4th, 2020 hoping to get included in the May Bioconductor release. It became 
apparent that approval would not be possible in time, as such I requested to 
expedite acceptance of CoreGx (on which the latter two packages depend) so it 
could be included. My reviewer obliged and I am thankful for that.

I was told to resubmit ToxicoGx and RadioGx on separate issues and that the 
review process would continue from where it was for the resubmissions. This 
occurred on April 25th, 2020. Before resubmission I had replied to a round of 
reviewer comments and was waiting for a reply before making more changes.

However, since resubmission I have received no further reviewer comments and no 
reply to my code updates since the last review. RadioGx will be a part of a 
workshop our lab is putting together for Bioconductor conference in July, but 
without acceptance of the package it will have to be installed from GitHub.

Additionally, ToxicoGx is the package that was used to curate data for our web 
application, ToxicoDB, which has been accepted to the NAR web server edition. 
We had assumed that the package would be accepted by now and have had criticism 
from our NAR reviewers about it's lack of availability. Both of these packages 
were available on CRAN before our submission to Bioconductor.

My question is, how do I move forward? Without response from my reviewer I do 
not know which conditions I need to meet for package acceptance? I am available 
to respond to criticism.

Initial submission of these packages occurred almost 2 months ago, and it has 
been over a month since the resubmissions. Is this normal? Are there 
extenuating circumstances of which I am unaware?

Our lab put a lot of time and effort into these packages and wish to share them 
with the Bioconductor community. Does anyone have advice on what I can do to 
get the ball rolling again?

Thanks for your assistance.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network




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Re: [Bioc-devel] To Push or Not To Push?

[Chris Eeles]

Hi Herve,

Thanks for the advice. We have been pretty thorough with our testing, so I 
think we will do a final check and push today.

Best,
Chris

Get Outlook for Android<https://aka.ms/ghei36>


From: Herv� Pag�s 
Sent: Saturday, April 25, 2020 11:25:25 PM
To: Chris Eeles ; Bioc-devel@r-project.org 

Cc: Smirnov, Petr 
Subject: Re: [Bioc-devel] To Push or Not To Push?

Hi Chris,

That is the question :-)

The last run of the builds got delayed (that's because we updated R to
final 4.0.0 on all build machines on Friday) so we weren't able to
update the report in time today with the results of the builds. Today's
builds have started already and I see that CoreGx is on the build
machines. So if everything goes as expected it should show up on
tomorrow's report.

I would say push your updates to PharmacoGx. HOWEVER, it's important
that you run R CMD build/check on PharmacoGx before you do so. Make sure
you use R 4.0.0 when you do this, that all your packages are up-to-date
(BiocManager::valid() will tell you that), and that you are using the
same version of CoreGx that is currently on the build machines (which is
the one at 'git clone 
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2FCoreGxdata=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435%7C1%7C0%7C637234683299229138sdata=qF2Ja1UekdeTjXDUfVR7aDRNY4RbfpsofFhn%2FDOqOAM%3Dreserved=0').
 If
every looks good then you can push with confidence.

Since today's builds have already started they won't pick up your
changes to PharmacoGx. But tomorrow's builds will. This means that you
won't be able to see the full picture before Monday's report. So yes,
that's kind of last minute but, again, if you're cautious before
pushing, everything should be fine ;-)

Cheers,
H.


On 4/25/20 17:27, Chris Eeles wrote:
> Hello Bioc-Devel community,
>
> We recently submitted CoreGx to Bioconductor and am happy to announce it was 
> accepted. However, the package has not yet made it into the 3.11 build and we 
> are concerned it may not make the release.
>
> Our existing Bioconductor package, PharmacoGx, has significant updates which 
> depend on CoreGx; thus we are hesitant to push our updates without CoreGx 
> being available in 3.11.
>
> I wonder if anyone can provide guidance on how best to move forward? We would 
> very much like to get the updated PharmacoGx into this release, but don't 
> want to risk releasing a package without a dependency. Should we push and 
> hope for the best or wait until tomorrow to see if we make the final build?
>
> Any advice would be appreciated.
>
> Thanks for your support.
>
> Best,
> ---
> Christopher Eeles
> Software Developer
> BHK 
> Laboratory<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.bhklab.ca_%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DLa4zNgzQBGQqABiXaILnttyOue2enaUkt_LSHyWgZFY%26s%3D9d3um0IkW59E0g04Fa5xFUEGdh-JKYmp18FB2kBZAVo%26e%3Ddata=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435%7C1%7C0%7C637234683299239127sdata=jmoPuh3fpo0%2FVRsk%2BdFDcprdjA0k6BA3I1I7XwyYBTY%3Dreserved=0
>  >
> Princess Margaret Cancer 
> Centre<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.pmgenomics.ca_pmgenomics_%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DLa4zNgzQBGQqABiXaILnttyOue2enaUkt_LSHyWgZFY%26s%3DZmT2DJ7Sv4CDUXyFY6lsScGGAR7rbD5P6kd0Mtn1EB0%26e%3Ddata=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435%7C1%7C0%7C637234683299239127sdata=%2BkaTUqADP3RZv3SinXhgnIxJuJGgpj9%2Fft5n2Gcf8Ak%3Dreserved=0
>  >
> University Health 
> Network<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.uhn.ca_%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DLa4zNgzQBGQqABiXaILnttyOue2enaUkt_LSHyWgZFY%26s%3DoB-YG0x2fv5AReP-wm78Uyt6jjN6d8-myJnIihcu-Po%26e%3Ddata=02%7C01%7C%7Cc60f0240a759498f15d708d7e9917836%7C84df9e7fe9f640afb435%7C1%7C0%7C637234683299239127sdata=P1GuVdfdzkjiqGIBxHbm%2By4qYnLZS3LPAMsY1IRZPxc%3Dreserved=0
>  >
>
>
>
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>
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[Bioc-devel] To Push or Not To Push?

[Chris Eeles]

Hello Bioc-Devel community,

We recently submitted CoreGx to Bioconductor and am happy to announce it was 
accepted. However, the package has not yet made it into the 3.11 build and we 
are concerned it may not make the release.

Our existing Bioconductor package, PharmacoGx, has significant updates which 
depend on CoreGx; thus we are hesitant to push our updates without CoreGx being 
available in 3.11.

I wonder if anyone can provide guidance on how best to move forward? We would 
very much like to get the updated PharmacoGx into this release, but don't want 
to risk releasing a package without a dependency. Should we push and hope for 
the best or wait until tomorrow to see if we make the final build?

Any advice would be appreciated.

Thanks for your support.

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network



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[Bioc-devel] Resubmitting additional packages as separate issues

[Chris Eeles]

Hello Bioc-devel,

I recently submitted three packages to Bioconductor Contributions (CoreGx, 
RadioGx and ToxicoGx). After consulting my reviewer I now wish to resubmit the 
two dependent packages (RadioGx and ToxicoGx) on separate issues. I deleted the 
comments from #1445 where I submitted the ‘additional packages’ on that issue, 
but I am now unable to resubmit the packages.

Could someone assist with this?

Best,
---
Christopher Eeles
Software Developer
BHK Laboratory
Princess Margaret Cancer Centre
University Health Network

From: bioc-issue-bot 
Sent: April 22, 2020 6:59 PM
To: Bioconductor/Contributions 
Cc: Christopher Eeles ; Mention 

Subject: Re: [Bioconductor/Contributions] (inactive) ToxicoGx resubmission 
(#1485)


Dear 
@ChristopherEeles
 ,

You (or someone) has already posted that repository to our tracker.

See 
#1445

You cannot post the same repository more than once.

If you would like this repository to be linked to issue number: 1485,
Please contact a Bioconductor Core Member.
I am closing this issue.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on 
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