[Bioc-devel] Reset to a previous commit

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 at 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]

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 at r-project.org on behalf of 
kasperdanielhansen at 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 at 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 at r-project.org>  on

behalf of

     > >>> Simon Dirmeier<simon.dirmeier at web.de>
     > >>> *Sent:* Monday, September 2, 2019 6:08:45 AM
     > >>> *To:*bioc-devel at r-project.org  <bioc-devel at 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]]
     > >>>
     > >>> _______________________________________________
     > >>> Bioc-devel at r-project.org  mailing list
     > >>>

     > 

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     > >>
     > >>
     > >> _______________________________________________
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     > >>

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https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8&s=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc&e=

     > > --
     > > Herv? Pag?s
     > >
     > > 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 at fredhutch.org
     > > Phone:  (206) 667-5791
     > > Fax:    (206) 667-1319

     >
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     --
     Best,
     Kasper

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