Hi, that's not the git way to do it. Your previous commit is already out in the open, if you git reset, that would be dangling in the air.
I really love this decision tree: https://sethrobertson.github.io/GitFixUm/fixup.html which in your case will get you probably to https://sethrobertson.github.io/GitFixUm/fixup.html#pushed_new_simple and "create an positive commit to remove the effects of a simple (non-merge) commit". Hope that helped, yours, Steffen On Tue, 2019-09-10 at 09:42 +0200, Simon Dirmeier wrote: > 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 -- Current bits of interest: * Köln Metabolomics Symposium 24.09.2019. Red meets green metabolomics http://metabolomics-cologne.eventbrite.de * European RFMF-Metabomeeting 2020 Toulouse, France, January 22-24 2020 https://rfmf-mpf-2020.sciencesconf.org --- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
