[Bioc-devel] Omada package failing due to removed dependency
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
<
That is, perhaps, not surprising... Package seems to be too good to be abandoned. I wonder if anyone
from
their lab <
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 <
LinkedIn:
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President
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LinkedIn:
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