Ant build of devel branch fails #43
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Thank you for the kind words and we are very happy that VizBin has proven useful for your research! @piotr-gawron could you please have a look a this? I am surprised by the `Total time: 583 minutes 13 seconds". IIRC, the compilations were typically quick and did not take almost 10 hours... |
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@iquasere, @claczny
Problem was gone when I switched to:
Of course I can imagine that you would like to use the latest java version. In such case you need to upgrade your ant. I tested it on I wasn't able to pinpoint exactly in which version they fixed the problem, but between ant 1.9.6 and ant 1.10.5 there are some bug fixes related to java 11. |
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Damn, those were fast answers and troubleshooting! The difference in versions would explain why it succeeded before, as the reformat was needed because of moving from 16.04 to 18.04. Problem is, ant is at the latest version, and still can't build VizBin. Java, however, is at 11.0.1, I'll update it and then attempt to build again |
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What do you mean ant is at the latest version? 1.10.5/1.9.14?? |
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I am using the latest versions of the tools. Still, it runs out of memory. I know barely nothing about ant (although this troubles have pushed me to learn some things) and I get this warning: |
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I have also confirmed it uses version 11.0.2 of java. |
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@iquasere, |
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Ubuntu 18.04.2 |
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dear @iquasere, However, I noticed one thing: the code that is cloned from repository contains Can you try the compilation with fresh clone from master branch? |
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I am cloning from devel branch, so I can use the CLI of VizBin. Does the master branch build allow for CLI usage? |
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Here is the command that shows that it's also working on Have you tried to run the compilation on clean system? Maybe you installed something on your ubuntu that interferes with java/ant? |
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Well, I have some ideas on what the problems were, but it seems to be just bad configuration on my end. Running apt-get install -y openjdk-11-jdk-headless failed, and it reported to lock files in /var. After some random attempts at solving that, sudo ant finally did the trick. This probably was a mixture of setting different javas, because the problems on /var persist. Now it compiles in 10 seconds. As it should be. Thank you very much for the valuable help! Gonna add it to my pipeline right now! Next publication, you gain one more reference ^^ |
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Well, the build went apparently fine. But when running VizBin... This means the ant build still didn't finished properly, right? A reformat on the system seems the only solution at this point... |
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Attempting to use the docker run also didn't work |
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Well, that's completely different question :). You explicitly asked about problems with ant build ;). Anyway, the full build process should start from top directory using make command. If you run it directly from the cloned repository it will probably not work due to:
I think Cedric forgot to document it... |
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Well, it started as an installation problem, but it has evolved xD Now, some months ago I ran the commands as they were specified in the issue concerning use through the command line. At that time, the tool was easily installed and used. Could it be that running it in Ubuntu 16.04 made the difference? Or maybe my system was already equiped with the libraries that it doesn't install by running ant from a sub-directory. |
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What made a difference is that before at the beginning you probably run the distribution jar (https://github.com/claczny/VizBin/blob/master/VizBin-dist.jar) which contained tsne. When run for the first time it extracts tsne into local folder on your computer. And after that you run the code from 'devel' branch. This compilation didn't contain tsne, however the tsne was already on your computer. Now, I assume that you are trying to compile and run it on clean machine. Therefore tsne is neither in the jar nor in the local system. And you get an error. |
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I don't think that is what is happening. finds some files Aren't these the files required? |
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And none of them is a compiled file for your OS. This is how it looks like after compilation for windows and linux: |
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@iquasere Not sure if the issue related to @piotr-gawron s comment
persists, but have you looked into https://github.com/claczny/VizBin/wiki/Minimal-Build-Environment already? Also, if there is anything you think could be made clearer in the documentation, please let us know - preferably in a separate issue ;) |
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Can you please confirm me if this works in your system? Must be used with some contigs.fasta file, but you probably have some available. |
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It doesn't work and as I mentioned before it shouldn't work. You don't compile the whole project with this command, but only java part. If you want to make it working like that try this, but it's hacky: There are three differences here:
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This was the part I was understanding, but had no knowledge to know how to do. But still, it does not work! Exactly same error as before! What do you mean by compiling only the java part? What is the docker command that makes VizBin work through the command line? |
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Let me try to clarify this :) VizBin combines a frontend (the data input/preprocessing and visualization component) with a backend (a C/C++-based program that implements BH-SNE). The frontend is programmed in Java and needs to be compiled using ant. The backend is programmed in C/C++ and needs to be compiled with a C/C++ compiler. These compilers differ by operating system, e.g, g++ from the Gnu Compiler Collection (GCC) in Linux. Compiling the C/C++ code results in a binary, which needs to be created for every OS separately. This is handled by the Makefile. Without these binaries, VizBin is incomplete. Hence, it is not sufficient to run the Java-compilation, but the C/C++-compilation should/must also occur. To facilitate this process, we have provided the Minimal Build Environment instructions. Have you looked into these? Moreover, I have to admit that I am a bit confused about the docker part that you are posting. Where did you find the respective descriptions? Hope this helps. Best, Cedric |
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The error persists if I do |
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Maybe a strange question, but have you tried simply running Your build process seems to be overly explicit. |
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Run make after all the previous commands, or on a fresh cloned repo? The error persists if simply |
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I would suggest a clean checkout -> switch to devel branch -> ensure you have the Minimal Build Environment set up -> |
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Does not work as |
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Could you please share if there are any errors/warnings reported and, if so, which? |
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The error reported has been the same every time |
Greetings
I used VizBin in the past, and it has never disappointed. It is a very good tool to visualize a spatial dispersion of the contigs, and very easy to install and use. However, I recently had to reformat my server, and when trying to reinstall VizBin as instructed in #15 , the ant build runs out of memory.
Since there have been no commits ever since I got this to work, I am wondering what could cause this problem. Has this been encountered when testing? I really would like to have this solved before integrating VizBin in my omics pipeline.
Thank you for your attention!
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