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