[Bioc-devel] Fwd: Re: Build error due to TensorFlow installation

Thu Sep 5 15:09:48 CEST 2019

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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> >>
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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
> > Seattle, WA 98109-1024
> >
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-- 
Best,
Kasper

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