subject:"Re\: \[Bioc\-devel\] Omada package failing due to removed dependency"

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

2024-04-02 Thread Sokratis Kariotis

23 at 9:44 AM Sokratis Kariotis <
>>>> >> > sokratiskario...@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 <
>>>> >> >> sokratiskario...@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.sheph...@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  on
>>>> behalf of
>>>> >> >>>> Sokratis Kariotis 
>>>> >> >>>> *Sent:* Monday, July 31, 2023 7:27 AM
>>>> >> >>>> *To:* Martin Grigorov 
>>>> >> >>>> *Cc:* bioc-devel@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.grigo...@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 <
>>>> >> >>>> > sokratiskario...@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:
>>>> >&

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

2024-04-01 Thread Sokratis Kariotis

Dear all,

I am getting some warnings that the Omada package is failing. If I am
correct I need to make some changes to both the devel and Release_3_18
branches. Because I am using a new laptop, could you let me know how to
make the necessary changes to fix both branches ( I mean how to connect and
upload my new code)? Thanks in advance!

Regards,
Dr. Sokratis Kariotis

On Fri, Feb 9, 2024 at 10:27 AM Sokratis Kariotis <
sokratiskario...@gmail.com> wrote:

> 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 
> 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 <
>> sokratiskario...@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  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 <
>>> > sokratiskario...@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.grigo...@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 <
>>> >> > sokratiskario...@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 <
>>> >> >> sokratiskario...@gmail.com> wrote:
>>> >> >>
>>> >> >>> Hey,
>>> >> >>>
>>> >> >>> I believe I have resolved the conflicts and now can run: *git push
>>> >

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

2024-02-09 Thread Mike Smith

gt;>> >> >>> 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.sheph...@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  on behalf
>>> of
>>> >> >>>> Sokratis Kariotis 
>>> >> >>>> *Sent:* Monday, July 31, 2023 7:27 AM
>>> >> >>>> *To:* Martin Grigorov 
>>> >> >>>> *Cc:* bioc-devel@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.grigo...@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 <
>>> >> >>>> > sokratiskario...@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),
>>> >> >>>>

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

2024-02-08 Thread Sokratis Kariotis

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 
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 <
> sokratiskario...@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  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 <
>> > sokratiskario...@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.grigo...@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 <
>> >> > sokratiskario...@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 <
>> >> >> sokratiskario...@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.sheph...@roswellpark.org> wrote:
>> >> >>>
>> >> >>>> You'll need to find the merge conflicts and resolve them. Recommit
>> >> >>>> those files and then it should go.
>> >> >>>>
>> >> >>>> Lori Shepherd - K

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

2023-09-12 Thread Lori Shepherd

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 <
sokratiskario...@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  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 <
> > sokratiskario...@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.grigo...@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 <
> >> > sokratiskario...@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 <
> >> >> sokratiskario...@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.sheph...@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  on behalf of
> >> >>>> Sokratis Kariotis 
> >> >>>> *Sent:* Monday, July 31, 2023 7:27 AM
> >> >>>> *To:* Martin Grigorov 
> >> >>>> *Cc:* bioc

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

2023-09-11 Thread Sokratis Kariotis

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  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 <
> sokratiskario...@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.grigo...@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 <
>> > sokratiskario...@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 <
>> >> sokratiskario...@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.sheph...@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  on behalf of
>> >>>> Sokratis Kariotis 
>> >>>> *Sent:* Monday, July 31, 2023 7:27 AM
>> >>>> *To:* Martin Grigorov 
>> >>>> *Cc:* bioc-devel@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.grigo...@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 <
>> >>>> > sokratiskario...@gmail.com> wrote:
>> >>>> >
>> >>>> >> Hey all,
>> >>>>

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

2023-08-17 Thread Mike Smith

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 
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  >
> 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 <
> > sokratiskario...@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 <
> >> sokratiskario...@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.sheph...@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  on behalf of
> >>>> Sokratis Kariotis 
> >>>> *Sent:* Monday, July 31, 2023 7:27 AM
> >>>> *To:* Martin Grigorov 
> >>>> *Cc:* bioc-devel@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.grigo...@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 <
> >>>> > sokratiskario...@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:*
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >>
&g

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

2023-08-16 Thread Sokratis Kariotis

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 
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 <
> sokratiskario...@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 <
>> sokratiskario...@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.sheph...@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  on behalf of
>>>> Sokratis Kariotis 
>>>> *Sent:* Monday, July 31, 2023 7:27 AM
>>>> *To:* Martin Grigorov 
>>>> *Cc:* bioc-devel@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.grigo...@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 <
>>>> > sokratiskario...@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:pack

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

2023-08-10 Thread Martin Grigorov

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 <
sokratiskario...@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 <
> sokratiskario...@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.sheph...@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  on behalf of
>>> Sokratis Kariotis 
>>> *Sent:* Monday, July 31, 2023 7:27 AM
>>> *To:* Martin Grigorov 
>>> *Cc:* bioc-devel@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, >> >
>>> 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 <
>>> > sokratiskario...@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 
>>> 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 distr

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

2023-08-10 Thread Sokratis Kariotis

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 
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 
> 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  on behalf of
>> Sokratis Kariotis 
>> *Sent:* Monday, July 31, 2023 7:27 AM
>> *To:* Martin Grigorov 
>> *Cc:* bioc-devel@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, 
>> 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 <
>> > sokratiskario...@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 
>> 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 <
>> >> > sokratiskario...@gmail.com> wrote:
>> >> >
>> >> >> Hey both,
>> >> >>
>> >> >> I have edited the package code but I'm having some difficulties
>> >> pushing it
>> >> >> to trigger

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

2023-08-01 Thread Mike Smith

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 
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  >
> 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  on behalf of
> > Sokratis Kariotis 
> > *Sent:* Monday, July 31, 2023 7:27 AM
> > *To:* Martin Grigorov 
> > *Cc:* bioc-devel@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,  >
> > 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 <
> > > sokratiskario...@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 
> wrote:
> > >>
> > >> > Hi Sokratis,
> > >> >
> > >> > Everything in Bioconductor is built around the central Bioconductor
> > git
> > >> > repositories.  The only

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

2023-08-01 Thread Sokratis Kariotis

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 
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  on behalf of
> Sokratis Kariotis 
> *Sent:* Monday, July 31, 2023 7:27 AM
> *To:* Martin Grigorov 
> *Cc:* bioc-devel@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, 
> 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 <
> > sokratiskario...@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  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 <
> >> > sokratiskario...@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.sheph...@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,
> >> >> >
> >> >>

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

2023-07-31 Thread Kern, Lori via Bioc-devel

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  on behalf of Sokratis 
Kariotis 
Sent: Monday, July 31, 2023 7:27 AM
To: Martin Grigorov 
Cc: bioc-devel@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, 
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 <
> sokratiskario...@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  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 <
>> > sokratiskario...@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.sheph...@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 
>> >> > *Sent:* Monday, July 10, 2023 10:27 AM
>> >> > *To:* Kern, Lori 
>> >> > *Cc:* Oleksii Nikolaienko ;
>> >> > bioc-devel@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

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

2023-07-31 Thread Sokratis Kariotis

Tried but its Already up to date.

On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, 
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 <
> sokratiskario...@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  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 <
>> > sokratiskario...@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.sheph...@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 
>> >> > *Sent:* Monday, July 10, 2023 10:27 AM
>> >> > *To:* Kern, Lori 
>> >> > *Cc:* Oleksii Nikolaienko ;
>> >> > bioc-devel@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.
>&

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

2023-07-31 Thread Martin Grigorov

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 <
sokratiskario...@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  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 <
> > sokratiskario...@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.sheph...@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 
> >> > *Sent:* Monday, July 10, 2023 10:27 AM
> >> > *To:* Kern, Lori 
> >> > *Cc:* Oleksii Nikolaienko ;
> >> > bioc-devel@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.sheph...@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 co

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

2023-07-31 Thread Sokratis Kariotis

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  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 <
> sokratiskario...@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 > >
>> 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 
>> > *Sent:* Monday, July 10, 2023 10:27 AM
>> > *To:* Kern, Lori 
>> > *Cc:* Oleksii Nikolaienko ;
>> > bioc-devel@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.sheph...@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
>>

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

2023-07-31 Thread Mike Smith

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 
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 
> 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 
> > *Sent:* Monday, July 10, 2023 10:27 AM
> > *To:* Kern, Lori 
> > *Cc:* Oleksii Nikolaienko ;
> > bioc-devel@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  >
> > 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@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 
> > *Sent:* Thursday, July 6, 2023 1:58 AM
> > *To:* Sokratis Kariotis 
> > *Cc:* Kern, Lori ;
> bioc-devel@r-project.org
> > 
> > *Subject:* Re: [Bioc-devel] Omada package failing due to removed
> > dependency
> >
> > https://nonstationarity.sciencesconf.org/resource/page/id/7
> > <
> 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
> >

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

2023-07-28 Thread Kern, Lori via Bioc-devel

Also of note,  When you push you will need to have a valid version bump but the 
build will not be triggered by a push instantly.  The daily builder will pull, 
build, check all packages only once a day.  The build report will show the 
version number and git commit id of what it last tried to use; and therefore if 
you miss the pull for today for instance, you would likely see it reflected 48 
hours after - if you made the commits before the pull for the day then it would 
be reflected in tomorrow's report.  I hope this helps.

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

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 
Sent: Friday, July 28, 2023 2:31 AM
To: Kern, Lori 
Cc: Oleksii Nikolaienko ; 
bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

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 
mailto:lori.sheph...@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 
mailto:sokratiskario...@gmail.com>>
Sent: Monday, July 10, 2023 10:27 AM
To: Kern, Lori 
Cc: Oleksii Nikolaienko 
mailto:oleksii.nikolaie...@gmail.com>>; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@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 
mailto:lori.sheph...@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@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 
mailto:oleksii.nikolaie...@gmail.com>>
Sent: Thursday, July 6, 2023 1:58 AM
To: Sokratis Kariotis 
mailto:sokratiskario...@gmail.com>>
Cc: Kern, Lori ; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

https://nonstationarity.sciencesconf.org/resource/page/id/7<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, pe

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

2023-07-28 Thread Kern, Lori via Bioc-devel

The package code needs to be pushed to git.bioconductor.org  not github.  Just 
wanted to be sure you are trying to push to the right place.  Could you please 
show the commands you are using with full output along with a git remote -v to 
make sure that is all set up correctly.
There are useful git workflows and help listed at:
 
http://contributions.bioconductor.org/git-version-control.html#essential-work-flow

If you are using a ssh key that was set up on github and reutilized for our 
credentials, that would be the passphrase you initially set up and not of our 
control.  If you cannot remember it you will have to create a new ssh key and 
upload it to the BiocCredentials app.  See some other possibilities at 
(specifically number 16)
http://contributions.bioconductor.org/git-version-control.html#faq

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 
Sent: Friday, July 28, 2023 2:31 AM
To: Kern, Lori 
Cc: Oleksii Nikolaienko ; 
bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

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 
mailto:lori.sheph...@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 
mailto:sokratiskario...@gmail.com>>
Sent: Monday, July 10, 2023 10:27 AM
To: Kern, Lori 
Cc: Oleksii Nikolaienko 
mailto:oleksii.nikolaie...@gmail.com>>; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@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 
mailto:lori.sheph...@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@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 
mailto:oleksii.nikolaie...@gmail.com>>
Sent: Thursday, July 6, 2023 1:58 AM
To: Sokratis Kariotis 
mailto:sokratiskario...@gmail.com>>
Cc: Kern, Lori ; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

https://nonstationarity.sciencesconf.org/resource/page/id/7<https://secure-web.cisco.com/1pCvxIL3lfzw2yMAoq1pXQ5JiavYeyZHI2qtDauHw4xwZZBxaV-dAKGWcVKgwz09vF4YJJGVvkcQloDj0mJOUxj7BI3WPu_1Ze3vDW0a9syxuRsiQNOGsRkJ8BaWBdlxOdRBAw39KujDDGqb_DPfL6IsjHK5UCqoCpzw39Gd

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

2023-07-28 Thread Sokratis Kariotis

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 
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 
> *Sent:* Monday, July 10, 2023 10:27 AM
> *To:* Kern, Lori 
> *Cc:* Oleksii Nikolaienko ;
> bioc-devel@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 
> 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@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 
> *Sent:* Thursday, July 6, 2023 1:58 AM
> *To:* Sokratis Kariotis 
> *Cc:* Kern, Lori ; bioc-devel@r-project.org
> 
> *Subject:* Re: [Bioc-devel] Omada package failing due to removed
> dependency
>
> https://nonstationarity.sciencesconf.org/resource/page/id/7
> <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 
> 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 
> wrote:
>
> We do not allow archived packages to be used.  All dependencies must be

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

2023-07-11 Thread Kern, Lori

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 
Sent: Monday, July 10, 2023 10:27 AM
To: Kern, Lori 
Cc: Oleksii Nikolaienko ; 
bioc-devel@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 
mailto:lori.sheph...@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@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 
mailto:oleksii.nikolaie...@gmail.com>>
Sent: Thursday, July 6, 2023 1:58 AM
To: Sokratis Kariotis 
mailto:sokratiskario...@gmail.com>>
Cc: Kern, Lori ; 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

https://nonstationarity.sciencesconf.org/resource/page/id/7<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 
mailto:sokratiskario...@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 
mailto:lori.sheph...@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

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

2023-07-10 Thread Sokratis Kariotis

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 
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@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 
> *Sent:* Thursday, July 6, 2023 1:58 AM
> *To:* Sokratis Kariotis 
> *Cc:* Kern, Lori ; bioc-devel@r-project.org
> 
> *Subject:* Re: [Bioc-devel] Omada package failing due to removed
> dependency
>
> https://nonstationarity.sciencesconf.org/resource/page/id/7
> <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 
> 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 
> 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  on behalf of
> Oleksii Nikolaienko 
> *Sent:* Thursday, June 29, 2023 5:36 AM
> *To:* Sokratis Kariotis 
> *Cc:* bioc-devel@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

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

2023-07-06 Thread Kern, Lori

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@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 
Sent: Thursday, July 6, 2023 1:58 AM
To: Sokratis Kariotis 
Cc: Kern, Lori ; bioc-devel@r-project.org 

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

https://nonstationarity.sciencesconf.org/resource/page/id/7<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 
mailto:sokratiskario...@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 
mailto:lori.sheph...@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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Oleksii Nikolaienko 
mailto:oleksii.nikolaie...@gmail.com>>
Sent: Thursday, June 29, 2023 5:36 AM
To: Sokratis Kariotis 
mailto:sokratiskario...@gmail.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@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 
mailto:sokratiskario...@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 a

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

2023-07-05 Thread Oleksii Nikolaienko

https://nonstationarity.sciencesconf.org/resource/page/id/7
That is, perhaps, not surprising...

Package seems to be too good to be abandoned. I wonder if anyone from their
lab <https://modalx.parisnanterre.fr/membres> could take over maintenance,
if you still bother to ask...

Best,
Oleksii

On Thu, 6 Jul 2023 at 06:23, Sokratis Kariotis 
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 
> 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  on behalf of
>> Oleksii Nikolaienko 
>> *Sent:* Thursday, June 29, 2023 5:36 AM
>> *To:* Sokratis Kariotis 
>> *Cc:* bioc-devel@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 <
>> sokratiskario...@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
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> >
>> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>
>> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0

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

2023-07-05 Thread Sokratis Kariotis

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 
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  on behalf of
> Oleksii Nikolaienko 
> *Sent:* Thursday, June 29, 2023 5:36 AM
> *To:* Sokratis Kariotis 
> *Cc:* bioc-devel@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 <
> sokratiskario...@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
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>


-- 
Cheers,
Sokratis Kariotis
PhD Student
University of Sheffield, M

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

2023-06-29 Thread Kern, Lori

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  on behalf of Oleksii 
Nikolaienko 
Sent: Thursday, June 29, 2023 5:36 AM
To: Sokratis Kariotis 
Cc: bioc-devel@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 
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
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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Re: [Bioc-devel] Omada package failing due to removed dependency

2023-06-29 Thread Oleksii Nikolaienko

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 
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: http://www.linkedin.com/in/sokratiskariotis
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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