[Bioc-devel] Omada package failing due to removed dependency

Hey,

Hope I find you well! I have pushed some changes in devel and (I believe)
in branch RELEASE_3_18. Could you check if it was done correctly and
whether it can reflect in the current available version? The updates were
minor but required for journal publication. Thanks!

Regards,
Dr. Sokratis Kariotis

On Wed, Sep 13, 2023 at 12:42?AM Lori Shepherd <shepherd.bioc at gmail.com>
wrote:

It would be great if you were able to also update the current release
RELEASE_3_17 branch so that the current users can use the package and so
that a broken version of the package is not saved for the Bioc 3.17 version
of packages.  But the package will be ok for the new release as long as it
is fixed in devel and will progate the fixed package at the end of October
to the new release.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center


On Mon, Sep 11, 2023 at 10:05?PM Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey,

Will the package be ok for the new release even though I still get the
same
error?

Cheers,
Sokratis

On Thu, Aug 17, 2023 at 3:38?PM Mike Smith <grimbough at gmail.com> wrote:

Hi Sokratis,

You've address the problems successfully in the devel branch (3.18) but
they remain in the release (3.17), so you're probably still getting the
messages relating to these builds (
https://bioconductor.org/checkResults/3.17/bioc-LATEST/omada/).

To fix this you'll need to checkout the RELEASE_3_17 branch, and then

make

the same changes you've already applied.  You can either do that via

git

cherry-pick and select the appropriate commits from devel branch, or
perhaps more straightforward is to just copy/paste the relevant

sections.

Then bump the RELEASE_3_17 version number to 1.2.1 and push that

branch.

Hopefully this will fix the issues there too.

Best,
Mike

On Thu, 17 Aug 2023 at 03:47, Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey all,

I can see all is green but I still get messages about failing builds

and

on
the website shows build error. Do I still have to do something?

Thanks in

advance.

Regards,
Sokratis

On Thu, Aug 10, 2023 at 2:53?PM Martin Grigorov <
martin.grigorov at gmail.com>
wrote:

Hi,

All is green at
https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/

Regards,
Martin

On Thu, Aug 10, 2023 at 9:44?AM Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey all,

Is this fixed now? I think I can see all pass, but on the actual

website

its still on error. Thanks!

Cheers,
Sokratis

On Tue, Aug 1, 2023 at 4:25?PM Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey,

I believe I have resolved the conflicts and now can run: *git push
upstream main:devel*
with Everything up-to-date as a result. However, *git push origin

main*

does not yield
anything and it keeps hanging without a message. I checked

https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/

and the last commit is April.


On Mon, Jul 31, 2023 at 10:01?PM Kern, Lori <
Lori.Shepherd at roswellpark.org> wrote:

You'll need to find the merge conflicts and resolve them.

Recommit

those files and then it should go.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf

of

Sokratis Kariotis <sokratiskariotis at gmail.com>
*Sent:* Monday, July 31, 2023 7:27 AM
*To:* Martin Grigorov <martin.grigorov at gmail.com>
*Cc:* bioc-devel at r-project.org <bioc-devel at r-project.org>
*Subject:* Re: [Bioc-devel] Omada package failing due to removed
dependency

Tried but its Already up to date.

On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, <
martin.grigorov at gmail.com>
wrote:

Hi Sokratis,

You need to do "git pull --rebase" before trying to push.
Most probably the version has been bumped upstream.

Regards,
Martin

On Mon, Jul 31, 2023 at 2:16?PM Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey all,

I created a new key and now I can commit etc but there is a

conflict

that

is not allowing me to go ahead.

My commands:
git add .
git commit -m "Update metrics"
git push upstream main:devel

*The above results in the following error:*













*Enumerating objects: 19, done.Counting objects: 100% (17/17),

done.Delta

compression using up to 16 threadsCompressing objects: 100%

(11/11),

done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s,

done.Total 11

(delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You

cannot push

without resolving merge conflicts.remote:remote: Please check

the

files in

the commit pushed to the git-serverremote: for merge conflict

markers like

'<<<<<<<', '========', '>>>>>>>'.remote:To
git.bioconductor.org:packages/omada ! [remote rejected] main

->

devel

(pre-receive hook declined)error: failed to push some refs to
'git.bioconductor.org:packages/omada'*



On Mon, Jul 31, 2023 at 3:36?PM Mike Smith <

grimbough at gmail.com>

wrote:

Hi Sokratis,

Everything in Bioconductor is built around the central

Bioconductor git

repositories.  The only way to get changes out to users is

to

commit

them

to git.bioconductor.org and then the build system will pick

those

up,

run

the tests and checks, create new versions of packages, and

make

them

available for distribution.

Perhaps you can include the git command you're running to

submit

the

changes and a copy of the exact error you're receiving.

That

might help

the team suggest a solution.

Best regards,
Mike

On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis <
sokratiskariotis at gmail.com> wrote:

Hey both,

I have edited the package code but I'm having some

difficulties

pushing it

to trigger another build (github passphrase). Is there

another

way to

trigger the build? Thanks!

Cheers,
Sokratis

On Wed, Jul 12, 2023 at 1:43?AM Kern, Lori <

Lori.Shepherd at roswellpark.org

wrote:

We can give you a little more time (a few weeks) to fix

the

package

but

please fix as soon as possible to avoid deprecation.

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Sokratis Kariotis <sokratiskariotis at gmail.com>
*Sent:* Monday, July 10, 2023 10:27 AM
*To:* Kern, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* Oleksii Nikolaienko <oleksii.nikolaienko at gmail.com

;

bioc-devel at r-project.org <bioc-devel at r-project.org>
*Subject:* Re: [Bioc-devel] Omada package failing due to

removed

dependency

Hey both,

I have checked the package license (GPL) and it should be

fine

to use

the

code. However, I am having difficulty finding the actual

code to

calculate

the internal metrics I am using (used in Omada's function
cluster_voting.R). I can only find the wrapper function

but

not

the

ones

that actually calculate the metrics. I am not sure how to

proceed

with

this

in time, so the Omada package won't get deprecated.

Regards,
Sokratis

On Fri, Jul 7, 2023 at 1:03?AM Kern, Lori <

Lori.Shepherd at roswellpark.org>

wrote:

We would not hunt down the lab especially for CRAN

packages,

but you

could reach out if you like.  That would probably be a

recommended

action

to either ask someone from their lab to maintain or if

you

are

willing

and

you really want the package around you could ask the lab

if

they mind

you

volunteering to be the new maintainer.

There could see two options for rewriting/maintaining.

1. Take over maintenance of the package and resubmit to

CRAN

It's a little tricky cause this is a CRAN package so I'm

not

sure on

their

exact policy of taking over an abandoned package. If

this is

desired,  I

would reach out to CRAN to find out their exact policy
2. Move needed code to your Bioconductor package
You'll have to check the original package license to make

sure

this

is

allowed under the license of the package. You will still

want

to give

the

original authors/maintainer credit. I would say to be

safe I

would

include

them as contributors/authors in the DESCRITPION Authors at R

field and

in

the R code I would add a comment above the code to

reference

original

package citation and stating it was copied from there.

I'm

not

a

lawyer or

license/copy right expert so not sure if that would be

good

enough

but

that

would be my take on it.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Oleksii Nikolaienko <

oleksii.nikolaienko at gmail.com>

*Sent:* Thursday, July 6, 2023 1:58 AM
*To:* Sokratis Kariotis <sokratiskariotis at gmail.com>
*Cc:* Kern, Lori <Lori.Shepherd at RoswellPark.org>;

bioc-devel at r-project.org

<bioc-devel at r-project.org>
*Subject:* Re: [Bioc-devel] Omada package failing due to

removed

dependency

https://secure-web.cisco.com/1EhksuB6k_yI--kj3_CN8LCovo7wAy9Epj-_8W4VV7FAbktome6nKnRrktDrrzsGXq6OrPZzxo7-CPAnrnZ4mFbi1Z-z81fIELFunE2pI8wuUlGU72f4Irnh1TjSXymZHtkM8_5OEv8EPAA1U7i6tUetGY5G8ZODgjnDQZaarKkEspvU92RNlxjLqzIKy-vIrX-TN-TtC-dDyaqOyIVUNZKJws7sU-V4VFjfkwoM5rK9BAdI4jIqcxygwdSeB5XsZftYZVy7nlTD1Rrp46lnGBMqvfBpVOQjd93wM9KQU1nafzbzIag4rrGGGlr_D4ZWB/https%3A%2F%2Fnonstationarity.sciencesconf.org%2Fresource%2Fpage%2Fid%2F7

<

https://secure-web.cisco.com/1pCvxIL3lfzw2yMAoq1pXQ5JiavYeyZHI2qtDauHw4xwZZBxaV-dAKGWcVKgwz09vF4YJJGVvkcQloDj0mJOUxj7BI3WPu_1Ze3vDW0a9syxuRsiQNOGsRkJ8BaWBdlxOdRBAw39KujDDGqb_DPfL6IsjHK5UCqoCpzw39GduVcBLFIutoPM8Nqjgp8ArDuh-oK-Bxe-huDYCoLXUX5GyU_fEG81AEtF-osCFtJNLRiQBggrsxcViF8mNihzVj8-UT4cNawHmz7xye_KNs45WZOxnVljiq5QQHuIGCeXRkbYBUvrpcEoTootlVxLloYK0/https%3A%2F%2Fnonstationarity.sciencesconf.org%2Fresource%2Fpage%2Fid%2F7

That is, perhaps, not surprising...

Package seems to be too good to be abandoned. I wonder if

anyone from

their lab
<

https://secure-web.cisco.com/1IisY82Mh0-7_0tTgq7v7MgjvGFKIBucg15oqE_SNpUPzwuvYYaCPgz427Efo9Xga7j3PYM6msIsM8GJAK7ofsjmhrfAG3_kBGCmTdF0gVYBUz17CdZjNygLUpDMXPSt6h5CfKAjX_SrymhwTWvvEuyH1cH3nCYhVkVd5xfdd2W5azA0g9MJ4bPASnxJwY9quFxu_6CAIuYXkkO_DqiO9NC6Nb22USMev1V4qh5A3IX2kg6l60sRbM9gDQWjNwbJAPSnWq9G5setIw9CNP8avnjON5nhm_cjNhhn6s6kY07wwiSQ4sSQqsekskzOjhbm1/https%3A%2F%2Fmodalx.parisnanterre.fr%2Fmembres

could take over maintenance, if you still bother to

ask...

Best,
Oleksii

On Thu, 6 Jul 2023 at 06:23, Sokratis Kariotis <

sokratiskariotis at gmail.com>

wrote:

Hey,

I haven't received any responses from the maintainer of

ClusterCrit

so I

guess I will have to re-write the code used. How can I

properly

go

about

this and credit the authors as well? Thanks!

Cheers,
Sokratis

On Thu, Jun 29, 2023 at 7:38?PM Kern, Lori <

Lori.Shepherd at roswellpark.org>

wrote:

We do not allow archived packages to be used.  All

dependencies

must

be

on

CRAN or Bioconductor. So yes if you can get them to

reinstate

the

package

on CRAN that would be ideal.  If not you will have to

remove

the

package

from the dependency list and either re-write the code

used

(giving

original

clusterCrit authors credit) or remove the functionality

used

from

that

package.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on

behalf of

Oleksii Nikolaienko <oleksii.nikolaienko at gmail.com>
*Sent:* Thursday, June 29, 2023 5:36 AM
*To:* Sokratis Kariotis <sokratiskariotis at gmail.com>
*Cc:* bioc-devel at r-project.org <bioc-devel at r-project.org

*Subject:* Re: [Bioc-devel] Omada package failing due to

removed

dependency

Hi,
in this case maybe it's worth reaching out to the

maintainer

of

clusterCrit. It was removed from CRAN because of

(seems-to-be)

minor

warnings, which can be addressed by the clusterCrit

developer

in no

time...

Best,
Oleksii

On Thu, 29 Jun 2023 at 08:44, Sokratis Kariotis <
sokratiskariotis at gmail.com>
wrote:

Dear Bioconductor team,

I received an email that my package "Omada" is failing

in

release

and

devel. I had a look and the problem seems to be:

*ERROR:

dependency

?clusterCrit? is not available for package ?omada?*.

So the

package

clusterCrit was removed. Is there a way I can use a

archived

version

of

it

(or something similar) so I don't have to rewrite code

based

on new

packages to avoid potentially inconsistencies? Please

advise,

thank

you!

Cheers,
Dr. Sokratis Kariotis (PhD)
Agency for Science, Technology and Research (A*STAR)
Singapore Immunology Network (SIgN)
Twitter: @s_kariotis <

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MedTech
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PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
Twitter: @s_kariotis <https://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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Cheers,
Sokratis Kariotis
PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
Twitter: @s_kariotis <https://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
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LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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Cheers,
Sokratis Kariotis
PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
Twitter: @s_kariotis <https://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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Cheers,
Sokratis Kariotis
PhD Student
University of Sheffield, Medical School
MedTech <https://www.facebook.com/medtechsheffield/>President
Twitter: @s_kariotis <https://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis