[Bioc-devel] Reset to a previous commit

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 at 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I've updated the link where the instructions are outdated.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 at 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 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]
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 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





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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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