how about TF for platforms that support it and C++ for those that don't, eventually migrating away from C++ as support grows? a little messy for the moment but let's get some mileage on the TF solution ASAP
On Thu, Sep 5, 2019 at 9:21 AM Dirmeier Simon <s...@simon-dirmeier.net> 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, 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-boun...@r-project.org> on behalf of > >>> Simon Dirmeier<simon.dirme...@web.de> > >>> *Sent:* Monday, September 2, 2019 6:08:45 AM > >>> *To:*bioc-devel@r-project.org <bioc-devel@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@r-project.org mailing list > >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8&s=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc&e= > > >>> > >>> This email message may contain legally privileged and/or confidential > >>> information. If you are not the intended recipient(s), or the employee > >>> or agent responsible for the delivery of this message to the intended > >>> recipient(s), you are hereby notified that any disclosure, copying, > >>> distribution, or use of this email message is prohibited. If you have > >>> received this message in error, please notify the sender immediately > >>> by e-mail and delete this email message from your computer. Thank you. > >> [[alternative HTML version deleted]] > >> > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> > 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= > > > -- > > 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 > > > > E-mail:hpa...@fredhutch.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
