[Bioc-devel] Reset to a previous commit

Turaga, Nitesh N|te@h@Tur@g@ @end|ng |rom Ro@we||P@rk@org
Tue Sep 10 16:45:33 CEST 2019 

Hi Simon,

I take this back actually. I think the best way forward is just undo the code changes, and add a new version number to it ( 1.9.3) and push. 

Step 1,

	Since your version 1.9.2 is already on Bioconductor, first sync your GitHub with that version.

Step 2,

	Undo the code changes, and add a new version 1.9.3 to it.

Step 3,

	You should be able to just do a regular push to Bioconductor here on out.

Best,

Nitesh 

> On Sep 10, 2019, at 8:51 AM, Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org> wrote:
> 
> Hi Simon,
> 
> Bioconductor's git system doesn't allow force push (This is a feature) .  It only allows a force push by administrators (Bioconductor Core team). Please send me a link to your GitHub repo which is at 1.9.0, and I will sync it for you.
> 
> I've updated the link where the instructions are outdated. Thank you for bringing this to our attention. 
> 
> Best,
> 
> Nitesh 
> 
>> On Sep 10, 2019, at 3:42 AM, Simon Dirmeier <simon.dirmeier using web.de> wrote:
>> 
>> Hi all,
>> following our previous TensorFlow discussion, I am trying to reset to a
>> previous commit and get rid of the TF changes in the meantime.Resetting
>> back to the last working commit [1] that doesn't use TF gives me this
>> error though:
>> 
>> $ git reset --hard 4e267949562a0b38b16495892c4ef4c0dcf7b6f3
>> 
>> 
>> $ git push -f upstream master
>> 
>> $ remote: Error: Illegal version bump from '1.9.2' to '1.9.0'. Check
>> $ remote: http://bioconductor.org/developers/how-to/version-numbering/
>> $ remote: for details
>> $ To git.bioconductor.org:packages/netReg.git
>> $  ! [remote rejected] master -> master (pre-receive hook declined)
>> $ error: failed to push some refs to
>> 'git using git.bioconductor.org:packages/netReg.git'
>> 
>> Trying to circumvent this by incrementing to '1.9.3' doesn't do the
>> trick either. Does anyone have any ideas how I could fix this issue?
>> 
>> Many thanks in advance again.
>> 
>> Best,
>> Simon
>> 
>> [1]
>> http://bioconductor.org/developers/how-to/git/abandon-changes/#reset-to-a-previous-commit
>> 
>> 
>> 
>> On 05.09.19 15:35, Martin Morgan wrote:
>>> I'm with Simon on the value of using TensorFlow here, and it's too bad the build system is unable to support more flexible use of python (there are additional challenges, for instance inter-operability between packages each depending on & starting their own python interpreter...)
>>> 
>>> It seems like the keras model
>>> 
>>> https://github.com/rstudio/keras
>>> https://keras.rstudio.com/
>>> 
>>> is reasonable -- providing an `install_keras()` and related convenience functions, but writing the package so that it does not depend on an available python for build & check. Obviously not checking the TensorFlow interface on a daily basis compromises the robustness of the software, and hopefully the build system will be able to provide a more robust testing environment in the future.
>>> 
>>> Martin
>>> 
>>> On 9/5/19, 9:10 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" <bioc-devel-bounces using r-project.org on behalf of kasperdanielhansen using gmail.com> wrote:
>>> 
>>>    It might be true that the code is much easier on your end, but it comes
>>>    with the complexity of using TensorFlow, which is a huge dependency. And
>>>    that library can be easy or impossible to install depending on your box.  I
>>>    am not saying people shouldn't use TensorFlow, but I am saying it brings a
>>>    lot of complexities with it.
>>> 
>>>    And (trying to) installing TensorFlow as part of .onLoad seems ... not the
>>>    right way to deal with this.
>>> 
>>>    On Thu, Sep 5, 2019 at 6:27 AM Simon Dirmeier <simon.dirmeier using web.de> wrote:
>>> 
>>>> 
>>>> Hi Herve,
>>>> 
>>>>> All this means that if you replace some old C++ code with TensorFlow
>>>>> then we will need to mark your package as unavailable on Windows and
>>>>> Mac, at least for now. Sorry. I wonder if there was something wrong
>>>>> with this old C++ code. I would recommend that you stick to it if you
>>>> can.
>>>>> 
>>>> The code is fine, but still an impractical complexity that doesn't need
>>>> to exist:
>>>> 
>>>> 1) It's hard to extend and read for others.
>>>> 
>>>> 2) It needs a custom configure.ac.
>>>> 
>>>> 3) Extending the package to other models/families is a huge pain, as one
>>>> needs to derive custom coordinate descents (or other optimizers for that
>>>> matter) for each.
>>>> 
>>>> On the other side:
>>>> 
>>>> 1) TF allowed me to replace like 5000 lines of source code with 100
>>>> lines of R.
>>>> 
>>>> 2) TF allows to easily extend with other models with just a few lines.
>>>> 
>>>> 3) I don't need a huge test suite.
>>>> 
>>>> 4) On GPUs it's a huge speedup.
>>>> 
>>>> So, I'll revert the changes back on Bioc devel for now and continue
>>>> development on another branch.
>>>> 
>>>> Cheers,
>>>> 
>>>> Simon
>>>> 
>>>> 
>>>> Am 04.09.19 um 16:53 schrieb Pages, Herve:
>>>>> 
>>>>> Hi Simon,
>>>>> 
>>>>> On 9/3/19 09:11, Simon Dirmeier wrote:
>>>>>> ...
>>>>>> Do you think it would be possible to install TensorFlow and
>>>>>> TensorFlow-Probability on the builders? I'd assume that many would
>>>>>> profit from that.
>>>>>> 
>>>>> As Lori mentioned at the end of her email (see below), we can't make
>>>>> the tensorflow Python module available on our Windows builders at the
>>>>> moment because we need to update Python to Python 3 on these machines
>>>>> first (AFAIK tensorflow is only available for Python 3 on Windows).
>>>>> This is something that we are currently working on.
>>>>> 
>>>>> As for the Mac builders, we have tensorflow there but unfortunately
>>>>> it's an old version because recent versions of are broken on El
>>>>> Capitan (this is the Mac OS version that, for various reasons, we are
>>>>> stuck with at the moment). This prevents us from installing the
>>>>> tensorflow_probability module which requires a recent version of
>>>>> tensorflow.
>>>>> 
>>>>> The tensorflow and tensorflow_probability modules are available on our
>>>>> Linux builders.
>>>>> 
>>>>> All this means that if you replace some old C++ code with TensorFlow
>>>>> then we will need to mark your package as unavailable on Windows and
>>>>> Mac, at least for now. Sorry. I wonder if there was something wrong
>>>>> with this old C++ code. I would recommend that you stick to it if you
>>>> can.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> H.
>>>>> 
>>>>> 
>>>>>>> Right now tensorflow is unavailable on our windows server (tokay1)�as
>>>>>>> we have not updated to python 3 (but will be in the near future)� The
>>>>>>> windows error can be ignored for now.
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 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-bounces using r-project.org>  on behalf of
>>>>>>> Simon Dirmeier<simon.dirmeier using web.de>
>>>>>>> *Sent:* Monday, September 2, 2019 6:08:45 AM
>>>>>>> *To:*bioc-devel using r-project.org  <bioc-devel using r-project.org>
>>>>>>> *Subject:* [Bioc-devel] Build error due to TensorFlow installation
>>>>>>> Dear all,
>>>>>>> 
>>>>>>> since I replaced some old C++ code with TensorFlow I am getting some
>>>>>>> build errors on merida1 and tokay1 regarding installation (even though
>>>> I
>>>>>>> install TF and TF Probability during /.onLoad/)
>>>>>>> 
>>>>>>> 
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_netReg_merida1-2Dbuildsrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8&s=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0&e=
>>>>>>> 
>>>>>>> Does anyone know how I can fix this or did anyone use TF with
>>>>>>> Bioconductor so far?
>>>>>>> 
>>>>>>> Many thanks in advance.
>>>>>>> 
>>>>>>> Best,
>>>>>>> 
>>>>>>> Simon
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> ������� [[alternative HTML version deleted]]
>>>>>>> 
>>>>>>> _______________________________________________
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>>>>>> 
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>>>>> --
>>>>> 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:hpages using fredhutch.org
>>>>> Phone:  (206) 667-5791
>>>>> Fax:    (206) 667-1319
>>>> 
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>>>> 
>>> 
>>> 
>>>    --
>>>    Best,
>>>    Kasper
>>> 
>>>    	[[alternative HTML version deleted]]
>>> 
>>>    _______________________________________________
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