[Bioc-devel] Build error due to TensorFlow installation

Thu, Sep 5, 2019 12:52 AM

Hi Herve,

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, for now I'll revert the changes back on Bioc devel and continue 
development on another branch.

Cheers,

S


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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[Bioc-devel] Build error due to TensorFlow installation

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