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

[Sokratis Kariotis]

Hey,

As an update, I managed to push the changes in devel (can see them in
https://code.bioconductor.org/browse/omada/commits/devel) but I am still
waiting for the build (
https://bioconductor.org/checkResults/3.19/bioc-LATEST/omada/) to go green.
After that happens I have to cherry-pick from devel to RELEASE_3_18 correct?

Cheers,
Sokratis

On Tue, Apr 2, 2024 at 11:06 AM Sokratis Kariotis <
sokratiskario...@gmail.com> wrote:

> 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, 20

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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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
> >
>
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>
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> Bioc-devel@r-project.org mailing list
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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
> 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

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

[Sokratis Kariotis]

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://twitter.com/s_kariotis>
LinkedIn: http://www.linkedin.com/in/sokratiskariotis

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Re: [Bioc-devel] Update existing packages and change name

[Sokratis Kariotis]

Hi all,

After lots of tries we decided to follow your second suggestion. How can we
stop the support for 32-bit windows?

Cheers,
Sokratis

On 22 March 2018 at 15:14, Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi Sokratis,
>
> On 03/22/2018 06:13 AM, Sokratis Kariotis wrote:
>
>>   Hey all,
>>
>> I have been updating my pathprint and pathprintGeoData packages (in 3.7)
>> and I encountered the following error in one of them (only on windows
>> server):
>>
>> Error: cannot allocate vector of size 237.3 Mb
>>
>> Here is the report: https://urldefense.proofpoint.
>> com/v2/url?u=https-3A__bioconductor.org_checkResults_3.7_
>> bioc-2DLATEST_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAv
>> imeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=vq6ajmYLDu1OVYL9MQ4KO2q
>> mc3ypMSQdmMTd3m4ygxY=kFbj_KW3LgfOmlyR4Pi4-ewT1wzqjOKnhdVUOB7u9xE=
>> pathprint/tokay2-checksrc.html
>>
>> How can I fix this? Thanks in advance.
>>
>
> Note that this error happens only when running the examples in 32-bit
> mode (arch i386) but not in 64-bit mode (arch x64). 32-bit Windows
> doesn't allow a process to use more than 2 Gb of RAM. There is no such
> limit with 64-bit Windows.
>
> You have 2 options: (1) reduce the memory footprint of the examples,
> or (2) give up on supporting your package for 32-bit Windows users.
>
> (2) should be the last resort.
>
> Cheers,
> H.
>
>
>
>> Cheers,
>> Sokratis
>>
>>
>> On 21 February 2018 at 20:37, Obenchain, Valerie <
>> valerie.obench...@roswellpark.org> wrote:
>>
>> Hi Sokratis,
>>>
>>> Unfortunately you can't rename a package ... and there is no such thing
>>> as
>>> a 'sub package'. Maybe you meant sub-package terms of dependencies. If
>>> you
>>> have new data to add that's independent of what's in pathprintGEOData you
>>> can create a new data package.
>>>
>>> I'm not sure what you mean by 'considerably more data'. The
>>> pathprintGEOData package is currently 22MG:
>>>
>>> ~ >du -h pathprintGEOData_1.4.0.tar.gz
>>> 22MpathprintGEOData_1.4.0.tar.gz
>>>
>>> We don't support git LFS yet in the experimental data repo. If you plan
>>> on
>>> making the package(s) very large we should consider making a
>>> ExperimentHub
>>> package where the data can be stored in S3.
>>>
>>> Valerie
>>>
>>>
>>>
>>> On 02/21/2018 05:16 AM, Sokratis Kariotis wrote:
>>>
>>> Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData)
>>> with
>>> considerably more data and a few code updates. I also want to change the
>>> name of the data package to reflect the new content. Can the package name
>>> be changed or do I have to create new sub-packages? Thanks in advance.
>>>
>>> Cheers
>>>
>>>
>>>
>>> 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.
>>>
>>
>>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>



-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Everything seems to be fine and the 3_6 release is online. Thanks for the
help!

Cheers,
Sokratis

On 5 April 2018 at 18:41, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:

> We are taking care of this on our end. Sorry for the confusion.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> *Sent:* Thursday, April 5, 2018 8:02:14 AM
> *To:* Shepherd, Lori
> *Cc:* Turaga, Nitesh; bioc-devel
>
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> Hey all,
>
> The issues remain the same in both packages:
>
> https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/
> malbec1-buildsrc.html
>
> https://bioconductor.org/checkResults/3.6/bioc-LATEST/
> pcxn/malbec1-buildsrc.html
>
> Regards,
> Sokratis
>
> On 30 March 2018 at 18:53, Shepherd, Lori <lori.sheph...@roswellpark.org>
> wrote:
>
> I believe this should clear up in a few days.  Because of the circular
> dependencies, it will require a few passes through the build system.
>
>
> For example:
>
>
> First pass:
>
> The pcxnData package has a force install, so it will get installed even
> if it fails the build and check. The pcxn package will also fail its first
> pass through.
>
>
> Second pass:
>
> the pcxn package will find the newly installed version of the pcxnData
> package and pass.  The pcxnData package will still fail
>
>
> Third pass:
>
> pcxnData will find the newly built software package and pass as will the
> linux version of the software package.
>
>
> Forth pass:
>
> May be needed for the mac and windows versions to find the new data
> package.
>
>
>
> The last update to the software package was on March 27 - which probably
> missed being pulled for the March 28th report so probably included for the
> March 29th build report
>
> March 29th  - both fail (but there was a force install behind the scenes)
>
> March 30th -  data package fails, but the linux version of the software
> package built and propagated
>
> http://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/
> malbec1-buildsrc.html
>
>
> My guess is that by Sunday's or Monday's build reports everything will be
> okay.
>
> I will keep an eye on this to make sure its the case and please let us
> know if you still are seeing issues next week.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> *Sent:* Thursday, March 29, 2018 6:49:47 AM
> *To:* Turaga, Nitesh
> *Cc:* Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> Hey all,
>
> The packages' changes went through to the 3_6 branch, but since pcxn and
> pcxnData depend on each other, there are errors when they get built as they
> see the old version of the other package. In the current example:
> https://www.bioconductor.org/checkResults/3.6/bioc-
> LATEST/pcxn/malbec1-buildsrc.html , the 
> pathCor_pathprint_v1.2.3_unadjusted_frame
> file is now located in the new pcxnData package but during build the old
> pcxnData is being used and the error occurs since the file is not there. I
> have checked both packages locally and they work when both are in their
> updated form. How can we bypass this? Thanks.
>
> Cheers,
> Sokratis
>
> On 27 March 2018 at 14:02, Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> wrote:
>
> Hey all,
>
> Thanks for the advice. I managed to fix the problem of no permissions! My
> windows machine, after an update, changed the paths to my github keys and
> had to reposition them.  I have now succesfully pushed in both master and
> RELEASE_3_6 branches.
>
> Cheers,
> Sokratis
>
> On 26 March 2018 at 15:47, Turaga, Nitesh <nitesh.tur...@roswellpark.org>
> wrote:
>
> Hi Sokratis,
>
> Your key(s) on file is
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp
> +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0
> Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL
> xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZ
> j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW
> cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvs

Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Hey all,

The issues remain the same in both packages:

https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/malbec1-buildsrc.html

https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html

Regards,
Sokratis

On 30 March 2018 at 18:53, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:

> I believe this should clear up in a few days.  Because of the circular
> dependencies, it will require a few passes through the build system.
>
>
> For example:
>
>
> First pass:
>
> The pcxnData package has a force install, so it will get installed even
> if it fails the build and check. The pcxn package will also fail its first
> pass through.
>
>
> Second pass:
>
> the pcxn package will find the newly installed version of the pcxnData
> package and pass.  The pcxnData package will still fail
>
>
> Third pass:
>
> pcxnData will find the newly built software package and pass as will the
> linux version of the software package.
>
>
> Forth pass:
>
> May be needed for the mac and windows versions to find the new data
> package.
>
>
>
> The last update to the software package was on March 27 - which probably
> missed being pulled for the March 28th report so probably included for the
> March 29th build report
>
> March 29th  - both fail (but there was a force install behind the scenes)
>
> March 30th -  data package fails, but the linux version of the software
> package built and propagated
>
> http://bioconductor.org/checkResults/3.6/bioc-LATEST/
> pcxn/malbec1-buildsrc.html
>
>
> My guess is that by Sunday's or Monday's build reports everything will be
> okay.
>
> I will keep an eye on this to make sure its the case and please let us
> know if you still are seeing issues next week.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> *Sent:* Thursday, March 29, 2018 6:49:47 AM
> *To:* Turaga, Nitesh
> *Cc:* Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> Hey all,
>
> The packages' changes went through to the 3_6 branch, but since pcxn and
> pcxnData depend on each other, there are errors when they get built as they
> see the old version of the other package. In the current example:
> https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-
> buildsrc.html , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now
> located in the new pcxnData package but during build the old pcxnData is
> being used and the error occurs since the file is not there. I have checked
> both packages locally and they work when both are in their updated form.
> How can we bypass this? Thanks.
>
> Cheers,
> Sokratis
>
> On 27 March 2018 at 14:02, Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> wrote:
>
> Hey all,
>
> Thanks for the advice. I managed to fix the problem of no permissions! My
> windows machine, after an update, changed the paths to my github keys and
> had to reposition them.  I have now succesfully pushed in both master and
> RELEASE_3_6 branches.
>
> Cheers,
> Sokratis
>
> On 26 March 2018 at 15:47, Turaga, Nitesh <nitesh.tur...@roswellpark.org>
> wrote:
>
> Hi Sokratis,
>
> Your key(s) on file is
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp
> +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0
> Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL
> xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZ
> j/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNW
> cEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+Q
> V5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6n
> FfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+
> rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80T
> a0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJ
> Yw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkB
> CHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2
> CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0
> UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR
> 2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8
> cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf
>
> s

Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Hey all,

The packages' changes went through to the 3_6 branch, but since pcxn and
pcxnData depend on each other, there are errors when they get built as they
see the old version of the other package. In the current example:
https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.htm
l , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now located in
the new pcxnData package but during build the old pcxnData is being used
and the error occurs since the file is not there. I have checked both
packages locally and they work when both are in their updated form. How can
we bypass this? Thanks.

Cheers,
Sokratis

On 27 March 2018 at 14:02, Sokratis Kariotis <s.kario...@sheffield.ac.uk>
wrote:

> Hey all,
>
> Thanks for the advice. I managed to fix the problem of no permissions! My
> windows machine, after an update, changed the paths to my github keys and
> had to reposition them.  I have now succesfully pushed in both master and
> RELEASE_3_6 branches.
>
> Cheers,
> Sokratis
>
> On 26 March 2018 at 15:47, Turaga, Nitesh <nitesh.tur...@roswellpark.org>
> wrote:
>
>> Hi Sokratis,
>>
>> Your key(s) on file is
>>
>> ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp
>> +v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0
>> Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacL
>> xxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1
>> CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/Ujrr
>> XanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLu
>> nUjQpVwqrnlHXcRGjkLB
>>
>> ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+Q
>> V5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6n
>> FfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+
>> rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80T
>> a0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJ
>> Yw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd
>>
>> ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkB
>> CHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2
>> CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0
>> UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR
>> 2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8
>> cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf
>>
>> ssh-rsa B3NzaC1yc2EDAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRt
>> Kf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/W
>> Z02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbvoZ3b9oPakFbQFiAtjPkN6h4
>> drr+iQq4to4jc5wvYw07uqIEEG8nZfiB+QWa5s+rplTS3zJZzr7xpEDT/7ZH
>> pKVduZUg34tzaN4+vONgofgOthUMWArO3oO69wPwAdoAUACRmXT02xknrcWZ
>> m4UtuhzT98FHLznSowZMLG3jm8vKgsgbH8UGGtz478UZW5xE4qS5LHiKJbcZ
>> FBCLFABUjCajuYF3z+bZF0cxbT9d+25kpp/p89lvljsvlE7vbxdqFmeobGS
>> Q6ftDq5btdEHfD2rc++iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9
>> sBL5gLFHTkl3KyxNdIsH9j0iNFdJmEHySZh2ePdrqG7ZE/FOKf77XTX+
>> acqgydF+Dsep16lTIxk94MXLk7Sz2v8XQqFtETa5q0Gkm70Ok/qht/O80nWU
>> T3QX44sPM4ivPckOHwnZjywpZyBONas26hP0M1pZSEvB5qLCMKyD4YmTJ5aZ
>> keCHh6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ==
>>
>> Are you sure you are using a private key which corresponds to any of
>> these public keys? I’d start with that.
>>
>> Best
>>
>> Nitesh
>>
>>
>> > On Mar 23, 2018, at 8:20 AM, Sokratis Kariotis <
>> s.kario...@sheffield.ac.uk> wrote:
>> >
>> > Hey Lori,
>> >
>> > While under the RELEASE_3_6 branch and using git fetch upstream or git
>> push
>> > upstream/RELEASE_3_6:
>> >
>> >
>> >
>> >
>> >
>> >
>> > *Warning: Permanently added 'git.bioconductor.org
>> > <http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of
>> known
>> > hosts.Permission denied (publickey).fatal: Could not read from remote
>> > repository.Please make sure you have the correct access rightsand the
>> > repository exists.*
>> >
>> >
>> > git remove -v results to:
>> >
>> >
>> >
>> >
>> >
>> >
>> > *origin  https://github.com/hidelab/pcxn.git
>> > <https://github.com/hidelab/pcxn.git> (fetch)origin
>> > https://github.com/hidelab/pcxn.git <https://github.com/hidelab/pc
>> xn.git>
>> > (push)upstreamg...@git.bioconductor.org:packages/pcxn.git
>> > (fetch)upstreamg...@git.bioconductor.org:packages/pcxn.git
>> (push)*
>> > The ssh command also gives:

Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Hey all,

Thanks for the advice. I managed to fix the problem of no permissions! My
windows machine, after an update, changed the paths to my github keys and
had to reposition them.  I have now succesfully pushed in both master and
RELEASE_3_6 branches.

Cheers,
Sokratis

On 26 March 2018 at 15:47, Turaga, Nitesh <nitesh.tur...@roswellpark.org>
wrote:

> Hi Sokratis,
>
> Your key(s) on file is
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+
> v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0O
> yl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/
> 02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+
> mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/
> UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk
> 9cLunUjQpVwqrnlHXcRGjkLB
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+
> QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6
> nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw
> +rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16
> k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtD
> xJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd
>
> ssh-rsa B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/
> uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogG
> QZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/
> kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/
> gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTl
> vTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/
> ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf
>
> ssh-rsa B3NzaC1yc2EDAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRt
> Kf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/
> WZ02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbvoZ3b9oPakFbQFiAtjPkN6h4drr+
> iQq4to4jc5wvYw07uqIEEG8nZfiB+QWa5s+rplTS3zJZzr7xpEDT/7ZHpKVduZUg34tzaN4+
> vONgofgOthUMWArO3oO69wPwAdoAUACRmXT02xknrcWZm4UtuhzT98FHLznS
> owZMLG3jm8vKgsgbH8UGGtz478UZW5xE4qS5LHiKJbcZFBCLFABUjCajuYF3
> z+bZF0cxbT9d+25kpp/p89lvljsvlE7vbxdqFmeobGSQ6ftDq5btdEHfD2rc++
> iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9sBL5gLFHTkl3KyxNdIs
> H9j0iNFdJmEHySZh2ePdrqG7ZE/FOKf77XTX+acqgydF+
> Dsep16lTIxk94MXLk7Sz2v8XQqFtETa5q0Gkm70Ok/qht/
> O80nWUT3QX44sPM4ivPckOHwnZjywpZyBONas26hP0M1pZSEvB5qLCMKyD4Y
> mTJ5aZkeCHh6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ==
>
> Are you sure you are using a private key which corresponds to any of these
> public keys? I’d start with that.
>
> Best
>
> Nitesh
>
>
> > On Mar 23, 2018, at 8:20 AM, Sokratis Kariotis <
> s.kario...@sheffield.ac.uk> wrote:
> >
> > Hey Lori,
> >
> > While under the RELEASE_3_6 branch and using git fetch upstream or git
> push
> > upstream/RELEASE_3_6:
> >
> >
> >
> >
> >
> >
> > *Warning: Permanently added 'git.bioconductor.org
> > <http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of
> known
> > hosts.Permission denied (publickey).fatal: Could not read from remote
> > repository.Please make sure you have the correct access rightsand the
> > repository exists.*
> >
> >
> > git remove -v results to:
> >
> >
> >
> >
> >
> >
> > *origin  https://github.com/hidelab/pcxn.git
> > <https://github.com/hidelab/pcxn.git> (fetch)origin
> > https://github.com/hidelab/pcxn.git <https://github.com/hidelab/pcxn.git
> >
> > (push)upstreamg...@git.bioconductor.org:packages/pcxn.git
> > (fetch)upstreamg...@git.bioconductor.org:packages/pcxn.git
> (push)*
> > The ssh command also gives:
> >
> >
> >
> >
> > *Warning: Permanently added 'git.bioconductor.org
> > <http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of
> known
> > hosts.Permission denied (publickey).*
> >
> > *Cheers,*
> >
> > *Sokratis*
> >
> >
> > On 23 March 2018 at 11:35, Shepherd, Lori <lori.sheph...@roswellpark.org
> >
> > wrote:
> >
> >> Where you able to update master?  Or are you having access trouble
> >> for both branches?  Please use reply all so that other members on the
> team
> >> can answer when appropriate and the responses go to the mailing list.
> >>
> >> Your package is in the git repository and has access with the ID
> s.kariotis.
> >> Can you please copy the commands with the output you are receiving that
> >> make you think that you do not have access?
> >>
> >> Please also include the output of
> >>
> >> git remote -v
> >>
> >> and
> >>
> >> ssh

Re: [Bioc-devel] Update data in data package, pcxnData

[Sokratis Kariotis]

Hey Lori,

While under the RELEASE_3_6 branch and using git fetch upstream or git push
upstream/RELEASE_3_6:






*Warning: Permanently added 'git.bioconductor.org
<http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of known
hosts.Permission denied (publickey).fatal: Could not read from remote
repository.Please make sure you have the correct access rightsand the
repository exists.*


git remove -v results to:






*origin  https://github.com/hidelab/pcxn.git
<https://github.com/hidelab/pcxn.git> (fetch)origin
https://github.com/hidelab/pcxn.git <https://github.com/hidelab/pcxn.git>
(push)upstreamg...@git.bioconductor.org:packages/pcxn.git
(fetch)upstreamg...@git.bioconductor.org:packages/pcxn.git (push)*
The ssh command also gives:




*Warning: Permanently added 'git.bioconductor.org
<http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of known
hosts.Permission denied (publickey).*

*Cheers,*

*Sokratis*


On 23 March 2018 at 11:35, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:

> Where you able to update master?  Or are you having access trouble
> for both branches?  Please use reply all so that other members on the team
> can answer when appropriate and the responses go to the mailing list.
>
> Your package is in the git repository and has access with the ID s.kariotis.
> Can you please copy the commands with the output you are receiving that
> make you think that you do not have access?
>
> Please also include the output of
>
> git remote -v
>
> and
>
> ssh -T g...@git.bioconductor.org
> (you should see RW access next to your package)
>
>
> Please
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of
> Shepherd, Lori <lori.sheph...@roswellpark.org>
> *Sent:* Friday, November 24, 2017 10:13 AM
> *To:* Sokratis Kariotis; bioc-devel
> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>
> You should make changes and push to the master branch of your package at
> g...@git.bioconductor.org:packages/pcxnData.git  .  This will update the
> devel version of your package.
>
> As long as the package builds correctly, It will be available for download
> immediately with Bioc devel 3.7.
>
>
> We don't encourage updating release unless it is a bug correction or
> justifiable updates, but if you push changes to the RELEASE_3_6 branch they
> will also be available in Bioc 3.6
>
>
> Instructions for pushing data to our git repository can be found here:
>
> http://bioconductor.org/developers/how-to/git/
>
>
> Remember to do a pull from our git repositories if you have not done so
> since the release as we update the versions when rolling out the release.
>
> http://bioconductor.org/developers/how-to/version-numbering/
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sokratis
> Kariotis <s.kario...@sheffield.ac.uk>
> Sent: Friday, November 24, 2017 10:02:13 AM
> To: bioc-devel
> Subject: [Bioc-devel] Update data in data package, pcxnData
>
> Hi all,
>
> I have a data package (pcxnData) that got released in 3.6 and I am
> wondering how long will it take, if I changed some of the data in that
> package for them to be publicly available in bioconductor instead of the
> old data. Can they be available sooner than the next release? Thanks in
> advance.
>
> Cheers,
> Sokratis Kariotis
>
>
>
> --
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ=gmail=g>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-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 h

Re: [Bioc-devel] Update existing packages and change name

[Sokratis Kariotis]

 Hey all,

I have been updating my pathprint and pathprintGeoData packages (in 3.7)
and I encountered the following error in one of them (only on windows
server):

Error: cannot allocate vector of size 237.3 Mb

Here is the report: https://bioconductor.org/checkResults/3.7/bioc-LATEST/
pathprint/tokay2-checksrc.html

How can I fix this? Thanks in advance.

Cheers,
Sokratis


On 21 February 2018 at 20:37, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Sokratis,
>
> Unfortunately you can't rename a package ... and there is no such thing as
> a 'sub package'. Maybe you meant sub-package terms of dependencies. If you
> have new data to add that's independent of what's in pathprintGEOData you
> can create a new data package.
>
> I'm not sure what you mean by 'considerably more data'. The
> pathprintGEOData package is currently 22MG:
>
> ~ >du -h pathprintGEOData_1.4.0.tar.gz
> 22MpathprintGEOData_1.4.0.tar.gz
>
> We don't support git LFS yet in the experimental data repo. If you plan on
> making the package(s) very large we should consider making a ExperimentHub
> package where the data can be stored in S3.
>
> Valerie
>
>
>
> On 02/21/2018 05:16 AM, Sokratis Kariotis wrote:
>
> Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData) with
> considerably more data and a few code updates. I also want to change the
> name of the data package to reflect the new content. Can the package name
> be changed or do I have to create new sub-packages? Thanks in advance.
>
> Cheers
>
>
>
> 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.




-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Update existing packages and change name

[Sokratis Kariotis]

Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData) with
considerably more data and a few code updates. I also want to change the
name of the data package to reflect the new content. Can the package name
be changed or do I have to create new sub-packages? Thanks in advance.

Cheers
-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Accepted packages can't find each other and fail build

[Sokratis Kariotis]

Hey all,

After the release I can see the release page of the pcxn package but not
pcxnData package. In the build page it says it cannot find the pcxn package
and fails.

Regards,
Sokratis

On 31 October 2017 at 16:33, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:

> It should be the same and you should be able to see the RELEASE_3_6 branch
>
>
> git fetch --all
>
> git branch -a
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> *Sent:* Tuesday, October 31, 2017 11:20:39 AM
> *To:* Shepherd, Lori
> *Cc:* Hervé Pagès; Obenchain, Valerie; bioc-devel
>
> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
> fail build
>
> Does the same hold for the pcxnData package? I can't see the RELEASE_3_6
> as in pcxn.
>
> -Sokratis
>
> On 31 October 2017 at 11:38, Shepherd, Lori <lori.sheph...@roswellpark.org
> > wrote:
>
>> The latest version bump change you made to 0.99.27 was yesterday Oct 30
>> right before we said to stop committing so we could make the release
>> branch.  That change did make it into both the RELEASE_3_6 and the master
>> branch and should appear in  the next build report for both versions.
>>
>>
>> Note:  It can take 12-24 hours to see version bumps and changes on the
>> build report. The daily builders runs once per day to build all the
>> packages; while a version bump is absolutely required, it is not built
>> instantaneously on a version bump.
>>
>>
>> Please be sure to pull from upstream before making further changes as we
>> have bumped the versions in both the release and devel versions of packages
>> for the release.
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
>> *Sent:* Tuesday, October 31, 2017 5:21:21 AM
>> *To:* Hervé Pagès
>> *Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel
>> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
>> fail build
>>
>> Hi all,
>>
>> There was an error in the pcxn package (and pcxnData as a resut of not
>> finding pcxn since it didnt build) which I fixed yesterday morning, but it
>> doesnt seem to accept my changes as the version in the build report is not
>> the last one I created but the erroneous one (2 days ago). I checked the
>> upstream of my package and it has my latest changes.
>>
>> Regards,
>> Sokratis
>>
>> On 27 October 2017 at 16:57, Hervé Pagès <hpa...@fredhutch.org> wrote:
>>
>>> Hi guys,
>>>
>>> On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
>>>
>>>> Hi Sokratis,
>>>>
>>>> I added the .BBSoptions file to pcxn when it should have been added to
>>>> pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
>>>> (not 'Depends') on the other. In this case it's pcxnData that needs the
>>>> .BBSoptions. Sorry for the mix up, this has been fixed.
>>>>
>>>> The data package should install with today's builds and be clean on the
>>>> Saturday report. The software package should then install with the Saturday
>>>> builds and be clean on the Sunday report.
>>>>
>>>>
>>> This is what should happen:
>>>
>>>   - pcxnData should install with today's data-exp builds (they
>>> started this morning) but vignette will still fail (pcxn still
>>> missing)
>>>
>>>   - pcxn won't install (will be back to NotNeeded) but should pass
>>> build/check and propagate on Saturday afternoon
>>>
>>>   - on Sunday morning, the data exp builds will find pcxn **on line**
>>> (because now it propagated) so will be able to install it so
>>> vignette will finally build and the package will propagate
>>>
>>> Thanks for taking care of this,
>>>
>>> H.
>>>
>>> Valerie
>>>>
>>>>
>>>> On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
>>>>
>>>> We have already taken care of this on our end

Re: [Bioc-devel] Accepted packages can't find each other and fail build

[Sokratis Kariotis]

Does the same hold for the pcxnData package? I can't see the RELEASE_3_6 as
in pcxn.

-Sokratis

On 31 October 2017 at 11:38, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:

> The latest version bump change you made to 0.99.27 was yesterday Oct 30
> right before we said to stop committing so we could make the release
> branch.  That change did make it into both the RELEASE_3_6 and the master
> branch and should appear in  the next build report for both versions.
>
>
> Note:  It can take 12-24 hours to see version bumps and changes on the
> build report. The daily builders runs once per day to build all the
> packages; while a version bump is absolutely required, it is not built
> instantaneously on a version bump.
>
>
> Please be sure to pull from upstream before making further changes as we
> have bumped the versions in both the release and devel versions of packages
> for the release.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis <s.kario...@sheffield.ac.uk>
> *Sent:* Tuesday, October 31, 2017 5:21:21 AM
> *To:* Hervé Pagès
> *Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
> fail build
>
> Hi all,
>
> There was an error in the pcxn package (and pcxnData as a resut of not
> finding pcxn since it didnt build) which I fixed yesterday morning, but it
> doesnt seem to accept my changes as the version in the build report is not
> the last one I created but the erroneous one (2 days ago). I checked the
> upstream of my package and it has my latest changes.
>
> Regards,
> Sokratis
>
> On 27 October 2017 at 16:57, Hervé Pagès <hpa...@fredhutch.org> wrote:
>
>> Hi guys,
>>
>> On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
>>
>>> Hi Sokratis,
>>>
>>> I added the .BBSoptions file to pcxn when it should have been added to
>>> pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
>>> (not 'Depends') on the other. In this case it's pcxnData that needs the
>>> .BBSoptions. Sorry for the mix up, this has been fixed.
>>>
>>> The data package should install with today's builds and be clean on the
>>> Saturday report. The software package should then install with the Saturday
>>> builds and be clean on the Sunday report.
>>>
>>>
>> This is what should happen:
>>
>>   - pcxnData should install with today's data-exp builds (they
>> started this morning) but vignette will still fail (pcxn still
>> missing)
>>
>>   - pcxn won't install (will be back to NotNeeded) but should pass
>> build/check and propagate on Saturday afternoon
>>
>>   - on Sunday morning, the data exp builds will find pcxn **on line**
>> (because now it propagated) so will be able to install it so
>> vignette will finally build and the package will propagate
>>
>> Thanks for taking care of this,
>>
>> H.
>>
>> Valerie
>>>
>>>
>>> On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
>>>
>>> We have already taken care of this on our end and you shouldn't need to
>>> do anything else.  As always changes reflected may take a few days to
>>> reflect in the build reports.
>>>
>>>
>>> The solution is to add a .BBSoptions file with ForceInstall: TRUE to the
>>> software package.  Since there is a circular dependency this will force
>>> install the software package even though there will be ERRORs because of
>>> the missing data package.  On the next build of the data packages, the data
>>> package will then successfully build finding the software package. Then
>>> following, the software package will also build finding the data package.
>>>
>>>
>>> Cheers,
>>>
>>>
>>> Lori Shepherd
>>>
>>> Bioconductor Core Team
>>>
>>> Roswell Park Cancer Institute
>>>
>>> Department of Biostatistics & Bioinformatics
>>>
>>> Elm & Carlton Streets
>>>
>>> Buffalo, New York 14263
>>>
>>> 
>>> From: Bioc-devel <bioc-devel-boun...@r-project.org>>> bioc-devel-boun...@r-project.org> on behalf of Sokratis Kariotis <
>>> s.kario...@sheffield.ac.uk><mailto:s.kario...@sheffield.ac.uk>

[Bioc-devel] Accepted packages can't find each other and fail build

[Sokratis Kariotis]

Hey all,

I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!

Cheers
-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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[Bioc-devel] new package submission (pcxn) Abnormal build result

[Sokratis Kariotis]

Hi all,

Today I submitted a new package called "pcxn" in bioconductor and I got the
following Abnormal built result:

Warning in fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics:
 chunk 4 (label = pcxn.network)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
  [tcl] invalid command name "font".

The pcxn.network function uses igraph::tkplot to return a network, which
works every time on several local machines. After searching for a while it
seems that whenever this problem arises its because of the igraph package
installation. How can I deal with this? Thanks in advance.

With Regards,
Sokratis
-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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[Bioc-devel] invalid PDF version and NULL vector errors in unchanged package

[Sokratis Kariotis]

Hey all,

I maintain 'pathprint', a package added to bioconductor in the last
release. Now the BioC 3.6 BUILD (
http://bioconductor.org/checkResults/3.6/bioc-LATEST/pathprint/)
 is
producing an error in all 3 platforms (despite it used to be error-free and
there were no changes to the code after that). *malbec1* and *tokay1* share
the same error:

Error: processing vignette 'exampleFingerprint.Rnw' failed with diagnostics:
invalid PDF version
Execution halted

while *veracruz1* provides a different error

Error: processing vignette 'exampleFingerprint.Rnw' failed with diagnostics:
 chunk 2 (label = data)
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  :
  'data' must be of a vector type, was 'NULL'
Execution halted

The two errors seem to be different, the first one appears at the very
beginning and is general,
while the second one is having a problem with the data chuck of the file.

Could any changes in BioC 3.6 be responsible, since the code didnt
change at all? Thanks in advance for any help!

Regards,

Sokratis

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Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Sokratis Kariotis]

Hey all,

Following your advice, the package now builds successfully! However, I got
this error while checking:

* checking package dependencies ... ERROR
Namespace dependency not required: ‘SummarizedExperiment’

Should I add *Imports :**SummarizedExperiment* in my DESCRIPTION file?

Regards,

Sokratis


On 30 March 2017 at 12:05, Martin Morgan <martin.mor...@roswellpark.org>
wrote:

> On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:
>
>> Hey all,
>>
>> Thanks for the input! I followed Marcel's advice and included the library
>> in my vignette. Also, I replaced lazyData with a datalist. The datalist
>> file includes "compressed_result : result" which is in turn loaded in the
>> vignette using "data(compressed_result)". However, I got:
>>
>> Warning in data(compressed_result) :
>>   data set ‘compressed_result’ not found
>>
>> Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
>> diagnostics:
>>  chunk 1
>> Error in assays(result) : object 'result' not found
>>
>
>
> I Stangle'd the vignette
>
>   cd pathprintGEOData/vignettes
>   R CMD Stangle usingPathprintGEOData.Rnw
>
> and then walked through the lines of R code. I got to
>
> > data(compressed_result)
> Warning message:
> In data(compressed_result) : data set 'compressed_result' not found
>
> The data 'compressed_result' is not found, because it is in the
> pathprintGEOData package, and the pathprintGEOData package is not on the
> search path.
>
> > search()
>  [1] ".GlobalEnv"   "package:SummarizedExperiment"
>  [3] "package:DelayedArray" "package:matrixStats"
>  [5] "package:Biobase"  "package:GenomicRanges"
>  [7] "package:GenomeInfoDb" "package:IRanges"
>  [9] "package:S4Vectors""package:BiocGenerics"
> [11] "package:parallel" "package:stats4"
> [13] "package:pathprint""ESSR"
> [15] "package:BiocInstaller""package:stats"
> [17] "package:graphics" "package:grDevices"
> [19] "package:utils""package:datasets"
> [21] "package:methods"  "Autoloads"
> [23] "package:base"
>
> It is not on the search path because, originally, pathprint had Depends:
> pathprintGEOData, but that was modified, as you know, to Suggests:
> pathprintGEOData, to avoid circular dependencies that thwart our build
> system. So previously library(pathprint) was enough to make the data
> available, but now you must either load the package
>
>   library(pathprintGEOData)
>   data(compressed_result)
>
> or tell data() where the data set is
>
>   data(compressed_result, package="pathprintGEOData")
>
> One would still like to use an informative name for the data (first
> argument of data) and presumably an identical name for the object that is
> loaded.
>
> Martin
>
>
>
>> So the dataset is still not loaded (again, these errors did not exist
>> prior to package acceptance). I have been using devtools to
>> build/check the package (since the github issue was closed) and these
>> warnings/errors dont show up, which imakes it difficult for me to fix
>> them. Thanks again for any input!
>>
>> Regards,
>>
>> Sokratis
>>
>>
>> On 27 March 2017 at 19:58, Michael Lawrence <lawrence.mich...@gene.com>
>> wrote:
>>
>> Actually, I don't see where the package itself is loaded in the
>>> vignette. If it were, this error would not occur.
>>>
>>> Unsurprisingly, I get this when trying to run the vignette code:
>>>
>>> Warning message:
>>> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>>>
>>> I noticed that pathprintGEOData just provides compressed_result, not
>>> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
>>> You might also consider turning off lazy data and using a datalist
>>> file for that package since the file is somewhat large.
>>>
>>> I also think that the datalist file for pathprint is out of date.
>>>
>>> Michael
>>>
>>> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
>>> <marcel.ramospe...@roswellpark.org> wrote:
>>>
>>>> Hi Sokratis,
>>>>
>>>> You can resolve this issue by moving `SummarizedExperiment` to the
>>>> Suggests field and
>>>>
>

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Sokratis Kariotis]

Hey all,

Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found

So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!

Regards,

Sokratis


On 27 March 2017 at 19:58, Michael Lawrence <lawrence.mich...@gene.com>
wrote:

> Actually, I don't see where the package itself is loaded in the
> vignette. If it were, this error would not occur.
>
> Unsurprisingly, I get this when trying to run the vignette code:
>
> Warning message:
> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>
> I noticed that pathprintGEOData just provides compressed_result, not
> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
> You might also consider turning off lazy data and using a datalist
> file for that package since the file is somewhat large.
>
> I also think that the datalist file for pathprint is out of date.
>
> Michael
>
> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
> <marcel.ramospe...@roswellpark.org> wrote:
> > Hi Sokratis,
> >
> > You can resolve this issue by moving `SummarizedExperiment` to the
> > Suggests field and
> >
> > including a `library(SummarizedExperiment)` call in your vignette.
> >
> > Best regards,
> >
> > Marcel
> >
> >
> > On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
> > <s.kario...@sheffield.ac.uk <mailto:s.kario...@sheffield.ac.uk>> wrote:
> >
> > Hey,
> >
> > I have submitted the package pathprintGEOData, which got accepted,
> > but the
> > build/check report is now producing the following error:
> >
> >
> >
> > *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
> > diagnostics:  chunk 1 Error in assays(result) : could not find
> function
> > "assays"*
> >
> > *assays *is a function from the SummarizedExperiment package which I
> > have
> > added on my Depends in DESCRIPTION. This error was not present during
> > building/checking before this package was accepted. Besides adding
> > SummarizedExperiment
> > to my Imports what else might be responsible for that error?
> >
> > Thank you for any help on the matter!
> >
> > -Sokratis
> >
> >  [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>mailing
> list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >
> > --
> > Marcel Ramos
> > Bioconductor Core Team Member
> > Roswell Park Cancer Institute
> >
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Sokratis Kariotis]

Hey,

I have submitted the package pathprintGEOData, which got accepted, but the
build/check report is now producing the following error:



*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics:  chunk 1 Error in assays(result) : could not find function
"assays"*

*assays *is a function from the SummarizedExperiment package which I have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?

Thank you for any help on the matter!

-Sokratis

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