[Bioc-devel] Build error due to TensorFlow installation

[Dirmeier Simon]

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, 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 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
>>>
>>>
>>>
>>>
>>>
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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
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>
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