[Bioc-devel] Reset to a previous commit
Simon Dirmeier
@|mon@d|rme|er @end|ng |rom web@de
Tue Sep 10 14:02:07 CEST 2019
Hi,
this is the way described in [1].
Cheers,
S
On 10.09.19 13:51, Neumann, Steffen wrote:
> Hi,
>
> that's not the git way to do it. Your previous commit is already
> out in the open, if you git reset, that would be dangling in the air.
>
> I really love this decision tree:
> https://sethrobertson.github.io/GitFixUm/fixup.html
>
> which in your case will get you probably to
> https://sethrobertson.github.io/GitFixUm/fixup.html#pushed_new_simple
>
> and "create an positive commit to remove the effects
> of a simple (non-merge) commit".
>
> Hope that helped,
> yours,
> Steffen
>
>
> On Tue, 2019-09-10 at 09:42 +0200, Simon Dirmeier 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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>>> > > --
>>> > > 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
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>>>
>>> --
>>> Best,
>>> Kasper
>>>
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