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

Tue, Aug 1, 2023 3:51 AM

Hi Sokratis,

You won't see an update in the build report for 24-48 hours.  The build
process happens at a specific time each day across all packages, you can't
trigger it manually, and the reports don't update until every package has
been built.  That takes about a day to complete.  If you're lucky and
commit just before the process starts it'll still be ~24 hours before you
see the results.  If you're unlucky and submit just after it'll be 2 days
before the changes are reflected in the report.

If you're interested, on
https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ there's a
section called "Snapshot Data" which tells you when the build process
started.  At the top of the page there's "This page was generated on" which
indicates when the report was posted.

However, you can check your commits have arrived in the repository by
taking a look at https://code.bioconductor.org/browse/omada/commits/devel
That site updates every 15 minutes, and I see three new commits in the last
day, so it looks like the git commands are working for you.  Now you can
just wait to see how the next report looks.

On Tue, 1 Aug 2023 at 10:26, 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

(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 <

https://secure-web.cisco.com/1EqWv8V2N5hRbw3HmoPEY8RdpEeWxqDoUa71DV8jQUiygXZiRjRxTOSFFWWDUSN7nw3Aviue7E_1xQuvbY4J8O3un4nvR0wtrlQUjMbs1vFGt5o9bI_InwlMvRWb2dhIe9ic0_2ugbdCwXwW_RGN1G4LJxUxm_yO9EkGSnc10bfG2fjit4oALm7Y8gMqnFusMJfqR3j-IKbu0Hem-jPRYXIeAurGmn1l7FvPYk9Pi6MHnOl1RN-5x19R655qOhP8vtsh9q-qwvckAbwuklQvq6lo0zKstGTdB6JkFCIIHswJrur4WrdjGMtwrYkWwOAQs/https%3A%2F%2Ftwitter.com%2Fs_kariotis

LinkedIn:

http://secure-web.cisco.com/1hrH0VDgCpCKm6BWl_eP9v57iZE2j6Y9RUetJ4RMrKylsFeYV7AWyeBfOewj6SpLxhrD-_JnI4sPdaUJB9Mwxuj-B5ot2FZIu4AU87ty04CdxW8zw9DShqtsaZPm68os9ySeI12kEcN_iujEcY11StQo1_qKeBsQchHO3Vc_qvfAbA2T29jSt4KX0OnG4UZENEfns3cigBqNgiYMOOiCGmz01_nIY5M3cgVbsTmSNA-pov7ZD6si4bOXF6pt-manBCeK0NB13icO5MMlpc8HNxSqkARD7n-R71Sa3ZsGQOIYPgA0uuuIRAR9DbV_F5kSj/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis

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

Thread (6 messages)