Re: [Bioc-devel] Fwd: Re: Build error due to TensorFlow installation
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 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 on behalf of > >>> Simon Dirmeier > >>> *Sent:* Monday, September 2, 2019 6:08:45 AM > >>> *To:*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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0= > >>> > >>> 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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc= > >>> > >>> This email message may contain legally privileged and/or confidential > >>> information. If
[Bioc-devel] Fwd: Re: Build error due to TensorFlow installation
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 on behalf of >>> Simon Dirmeier >>> *Sent:* Monday, September 2, 2019 6:08:45 AM >>> *To:*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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0= >>> >>> 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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc= >>> >>> 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 >>
