Hi all, following our previous TensorFlow discussion, I am trying to reset to a previous commit and get rid of the TF changes in the meantime.Resetting back to the last working commit [1] that doesn't use TF gives me this error though:
$ git reset --hard 4e267949562a0b38b16495892c4ef4c0dcf7b6f3 $ git push -f upstream master $ remote: Error: Illegal version bump from '1.9.2' to '1.9.0'. Check $ remote: http://bioconductor.org/developers/how-to/version-numbering/ $ remote: for details $ To git.bioconductor.org:packages/netReg.git $ ! [remote rejected] master -> master (pre-receive hook declined) $ error: failed to push some refs to 'g...@git.bioconductor.org:packages/netReg.git' Trying to circumvent this by incrementing to '1.9.3' doesn't do the trick either. Does anyone have any ideas how I could fix this issue? Many thanks in advance again. Best, Simon [1] http://bioconductor.org/developers/how-to/git/abandon-changes/#reset-to-a-previous-commit On 05.09.19 15:35, Martin Morgan wrote: > I'm with Simon on the value of using TensorFlow here, and it's too bad the > build system is unable to support more flexible use of python (there are > additional challenges, for instance inter-operability between packages each > depending on & starting their own python interpreter...) > > It seems like the keras model > > https://github.com/rstudio/keras > https://keras.rstudio.com/ > > is reasonable -- providing an `install_keras()` and related convenience > functions, but writing the package so that it does not depend on an available > python for build & check. Obviously not checking the TensorFlow interface on > a daily basis compromises the robustness of the software, and hopefully the > build system will be able to provide a more robust testing environment in the > future. > > Martin > > On 9/5/19, 9:10 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" > <bioc-devel-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com> > wrote: > > 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.dirme...@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-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 > > > > > -- > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
