Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Thanks for fixing this Nitesh and Sam!
I wrote that R check and forgot that it depended on the Gencode url. I
had to fix this too for recount
https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e.
Best,
Leo
On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh
wrote:
>
> Hi Sam,
>
> I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the
> commit history for RELEASE_3_8 though, (which I fixed in
> git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in
> rafalab/bumphunter.
>
> The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
>
> 7437f04 Apply interval bugfix to sanitized master branch
> a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8
> branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> The commit showing "bump x.y.z versions to odd y after creation of
> RELEASE_3_8 branch” should not be in the RELEASE_3_8 branch. The version
> number in the RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z
> version numbering scheme.
>
> After fixing your RELEASE_3_8 branch now looks like this,
>
> 96fd715 Bump version after cherry-picking bug fix,
> ac34111 Apply interval bugfix to sanitized master branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should
> now build on RELEASE_3_8 if the fix works.
>
> NOTE: After a push is made it can take up to 48 hours for it to
> appear on the build report and landing pages - i.e. we do one pull,
> build, check, propagate in 24 hours - so if your commit was after the pull
> for the day it wont be until the following day
>
>
> Best,
>
> Nitesh
>
>
> > On Nov 5, 2018, at 2:56 PM, Samuela Pollack
> > wrote:
> >
> > Hi Nitesh,
> >
> > I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch,
> > and request synchronization with Bioconductor RELEASE_3_8. We need this,
> > because bumphunter is not building on RELEASE_3_8, due to an obsolete URL
> > in one of the tests.
> >
> > thanks,
> >
> > - Sam
> >
> >
> > On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
> >> External Email - Use Caution
> >>
> >> Hi Sam,
> >>
> >> I have updated your “master” branch on git.bioconductor.com to reflect
> >> what you have on GitHub, at https://github.com/rafalab/bumphunter. You
> >> will not get the duplicate commit error when you push to the master branch
> >> anymore.
> >>
> >> However, RELEASE_3_8 still has duplicate commits in the history. You could
> >> follow the same procedure as you did for the master branch, and
> >> de-duplicate the commit history for RELEASE_3_8. You should invest time in
> >> this only if you think there will be any changes made to the release
> >> branch. If not, then this is not an issue. If you do choose to follow
> >> through with RELEASE_3_8 as well, please reply to this thread when you
> >> have made the de-duplication changes and added the branch to your GitHub
> >> repository.
> >>
> >> Best regards,
> >>
> >> Nitesh
> >>
> >>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
> >>> wrote:
> >>>
> >>> Dear Bioconductor,
> >>>
> >>> I believe I have removed all duplicate commits from the bumphunter
> >>> package. The main branch in rafalab/bumphunter incorporates the new
> >>> commit history. It passes 'library(devtools); build("."); install();
> >>> check("."); BiocCheck(".")'
> >>>
> >>> I am contacting you in accordance with item 6 of the instructions at this
> >>> URL:
> >>> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
> >>>
> >>> - Sam
> >>>
> >>> ___
> >>> 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 have
> >> received this message in error, please notify the sender immediately by
> >> e-mail and delete this email message from your computer. Thank you.
> >
>
>
>
> 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.
> ___
> Bioc-devel@r-project.org mailing list
Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Sam,
I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the
commit history for RELEASE_3_8 though, (which I fixed in
git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in
rafalab/bumphunter.
The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
7437f04 Apply interval bugfix to sanitized master branch
a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8
branch
3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
The commit showing "bump x.y.z versions to odd y after creation of RELEASE_3_8
branch” should not be in the RELEASE_3_8 branch. The version number in the
RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z version numbering
scheme.
After fixing your RELEASE_3_8 branch now looks like this,
96fd715 Bump version after cherry-picking bug fix,
ac34111 Apply interval bugfix to sanitized master branch
3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should now
build on RELEASE_3_8 if the fix works.
NOTE: After a push is made it can take up to 48 hours for it to
appear on the build report and landing pages - i.e. we do one pull,
build, check, propagate in 24 hours - so if your commit was after the pull
for the day it wont be until the following day
Best,
Nitesh
> On Nov 5, 2018, at 2:56 PM, Samuela Pollack
> wrote:
>
> Hi Nitesh,
>
> I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch,
> and request synchronization with Bioconductor RELEASE_3_8. We need this,
> because bumphunter is not building on RELEASE_3_8, due to an obsolete URL in
> one of the tests.
>
> thanks,
>
> - Sam
>
>
> On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
>> External Email - Use Caution
>>
>> Hi Sam,
>>
>> I have updated your “master” branch on git.bioconductor.com to reflect what
>> you have on GitHub, at https://github.com/rafalab/bumphunter. You will not
>> get the duplicate commit error when you push to the master branch anymore.
>>
>> However, RELEASE_3_8 still has duplicate commits in the history. You could
>> follow the same procedure as you did for the master branch, and de-duplicate
>> the commit history for RELEASE_3_8. You should invest time in this only if
>> you think there will be any changes made to the release branch. If not, then
>> this is not an issue. If you do choose to follow through with RELEASE_3_8 as
>> well, please reply to this thread when you have made the de-duplication
>> changes and added the branch to your GitHub repository.
>>
>> Best regards,
>>
>> Nitesh
>>
>>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
>>> wrote:
>>>
>>> Dear Bioconductor,
>>>
>>> I believe I have removed all duplicate commits from the bumphunter package.
>>> The main branch in rafalab/bumphunter incorporates the new commit history.
>>> It passes 'library(devtools); build("."); install(); check(".");
>>> BiocCheck(".")'
>>>
>>> I am contacting you in accordance with item 6 of the instructions at this
>>> URL:
>>> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
>>>
>>> - Sam
>>>
>>> ___
>>> 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 have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>
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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Nitesh,
I have fixed the commit history for rafalab/bumphunter RELEASE_3_8
branch, and request synchronization with Bioconductor RELEASE_3_8. We
need this, because bumphunter is not building on RELEASE_3_8, due to an
obsolete URL in one of the tests.
thanks,
- Sam
On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
External Email - Use Caution
Hi Sam,
I have updated your “master” branch on git.bioconductor.com to reflect what you
have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the
duplicate commit error when you push to the master branch anymore.
However, RELEASE_3_8 still has duplicate commits in the history. You could
follow the same procedure as you did for the master branch, and de-duplicate
the commit history for RELEASE_3_8. You should invest time in this only if you
think there will be any changes made to the release branch. If not, then this
is not an issue. If you do choose to follow through with RELEASE_3_8 as well,
please reply to this thread when you have made the de-duplication changes and
added the branch to your GitHub repository.
Best regards,
Nitesh
On Nov 2, 2018, at 5:09 PM, Samuela Pollack wrote:
Dear Bioconductor,
I believe I have removed all duplicate commits from the bumphunter package. The main branch in
rafalab/bumphunter incorporates the new commit history. It passes 'library(devtools); build(".");
install(); check("."); BiocCheck(".")'
I am contacting you in accordance with item 6 of the instructions at this URL:
http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
- Sam
___
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 have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Sam,
I have updated your “master” branch on git.bioconductor.com to reflect what you
have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the
duplicate commit error when you push to the master branch anymore.
However, RELEASE_3_8 still has duplicate commits in the history. You could
follow the same procedure as you did for the master branch, and de-duplicate
the commit history for RELEASE_3_8. You should invest time in this only if you
think there will be any changes made to the release branch. If not, then this
is not an issue. If you do choose to follow through with RELEASE_3_8 as well,
please reply to this thread when you have made the de-duplication changes and
added the branch to your GitHub repository.
Best regards,
Nitesh
> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
> wrote:
>
> Dear Bioconductor,
>
> I believe I have removed all duplicate commits from the bumphunter package.
> The main branch in rafalab/bumphunter incorporates the new commit history. It
> passes 'library(devtools); build("."); install(); check("."); BiocCheck(".")'
>
> I am contacting you in accordance with item 6 of the instructions at this
> URL: http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
>
> - Sam
>
> ___
> 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 have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
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[Bioc-devel] Request upstream pull --force of sanitized master branch
Dear Bioconductor,
I believe I have removed all duplicate commits from the bumphunter
package. The main branch in rafalab/bumphunter incorporates the new
commit history. It passes 'library(devtools); build("."); install();
check("."); BiocCheck(".")'
I am contacting you in accordance with item 6 of the instructions at
this URL:
http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
- Sam
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
