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
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
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
on
the website shows build error. Do I still have to do something? Thanks
advance.
Regards,
Sokratis
On Thu, Aug 10, 2023 at 2:53?PM Martin Grigorov <
martin.grigorov at gmail.com>
wrote:
Hey all,
Is this fixed now? I think I can see all pass, but on the actual
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
does not yield
anything and it keeps hanging without a message. I checked
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
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
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),
compression using up to 16 threadsCompressing objects: 100%
done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s,
(delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You
without resolving merge conflicts.remote:remote: Please check
the commit pushed to the git-serverremote: for merge conflict
'<<<<<<<', '========', '>>>>>>>'.remote:To
git.bioconductor.org:packages/omada ! [remote rejected] main
(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 <
Hi Sokratis,
Everything in Bioconductor is built around the central
repositories. The only way to get changes out to users is to
to git.bioconductor.org and then the build system will pick
the tests and checks, create new versions of packages, and
available for distribution.
Perhaps you can include the git command you're running to
changes and a copy of the exact error you're receiving. That
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
to trigger another build (github passphrase). Is there
trigger the build? Thanks!
Cheers,
Sokratis
On Wed, Jul 12, 2023 at 1:43?AM Kern, Lori <
Lori.Shepherd at roswellpark.org
We can give you a little more time (a few weeks) to fix
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
dependency
Hey both,
I have checked the package license (GPL) and it should be
code. However, I am having difficulty finding the actual
the internal metrics I am using (used in Omada's function
cluster_voting.R). I can only find the wrapper function
that actually calculate the metrics. I am not sure how to
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
could reach out if you like. That would probably be a
to either ask someone from their lab to maintain or if you
you really want the package around you could ask the lab
volunteering to be the new maintainer.
There could see two options for rewriting/maintaining.
1. Take over maintenance of the package and resubmit to
It's a little tricky cause this is a CRAN package so I'm
exact policy of taking over an abandoned package. If this
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
allowed under the license of the package. You will still
original authors/maintainer credit. I would say to be
them as contributors/authors in the DESCRITPION Authors at R
the R code I would add a comment above the code to
package citation and stating it was copied from there.
license/copy right expert so not sure if that would be
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
That is, perhaps, not surprising...
Package seems to be too good to be abandoned. I wonder if
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
guess I will have to re-write the code used. How can I
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
CRAN or Bioconductor. So yes if you can get them to
on CRAN that would be ideal. If not you will have to
from the dependency list and either re-write the code used
clusterCrit authors credit) or remove the functionality
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
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
dependency
Hi,
in this case maybe it's worth reaching out to the
clusterCrit. It was removed from CRAN because of
warnings, which can be addressed by the clusterCrit
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
devel. I had a look and the problem seems to be: *ERROR:
?clusterCrit? is not available for package ?omada?*. So
clusterCrit was removed. Is there a way I can use a
(or something similar) so I don't have to rewrite code
packages to avoid potentially inconsistencies? Please
Cheers,
Dr. Sokratis Kariotis (PhD)
Agency for Science, Technology and Research (A*STAR)
Singapore Immunology Network (SIgN)
Twitter: @s_kariotis <
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