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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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error installing in Ubuntu 16.04 #1984

Open nllg opened 5 years ago

nllg commented 5 years ago

Please describe:

  1. What you were trying to do
  2. What you wanted to happen
  3. What actually happened
  4. What data and command line to use to make the problem recur, if applicable
Format code blocks or terminal copy-pastes like this, between triple backticks.
nllg commented 5 years ago

Hello,

I am trying to install vg in my Ubuntu 16.04 I followed the instructions: git clone --recursive https://github.com/vgteam/vg.git

I get the following error: fatal: unable to connect to sourceware.org fatal: clone of 'git://sourceware.org/git/elfutils.git' into submodule path 'deps/elfutils' failed

Do you have any suggestions?

Thank you,

Nathaly

adamnovak commented 5 years ago

Hello,

I've just tried the command you tried, and it currently works for me. I suspect that sourceware.org, which hosts one of our dependencies, may have been down when you ran the command.

Can you try the same command again?

steinbrl commented 4 years ago

Hi,

I got the same error: clone of deps/elfutils failed

The git page is not down. It is possible to navigate manually to this page. I don't see the problem.

Do you have any suggestions?

Greetings,

Lars

adamnovak commented 4 years ago

Hello @steinbrl

I just did a git clone git://sourceware.org/git/elfutils.git and it seemed to work. Maybe Sourceware was misconfigured, or was down when you cloned but not when you went to the web page? What happens if you rm -Rf deps/elfutils and git submodule update --init --recursive now?

If that still doesn't work, and you can still get to Sourceware's web pages, what happens if you go to some other folder and try to git clone --verbose git://sourceware.org/git/elfutils.git? Does it give any more information on why it can't clone the repo beyond just that it failed? (Like a complaint that you are out of disk space or something?)

If this keeps happening to people, maybe we should host a mirror of the Sourceware repo on Github and point to that, so that if it's down, it's a Big Event and not an apparent bug in our repo.

ekg commented 4 years ago

Are our releases including tarballs?

On Tue, Dec 10, 2019 at 11:42 PM Adam Novak notifications@github.com wrote:

Hello @steinbrl https://github.com/steinbrl

I just did a git clone git://sourceware.org/git/elfutils.git and it seemed to work. Maybe Sourceware was down, or the git part of it was dfown, but it came back up? What happens if you rm -Rf deps/elfutils and git submodule update --init --recursive?

If that still doesn't work, and you can still get to Sourceware's web pages, what happens if you go to some other folder and try to git clone --verbose git://sourceware.org/git/elfutils.git? Does it give any more information on why it can't clone the repo beyond just that it failed? (Like a complaint that you are out of disk space or something?)

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adamnovak commented 4 years ago

Yeah, that's another option. The latest one is https://github.com/vgteam/vg/releases/download/v1.20.0/vg-v1.20.0.tar.gz and it comes with all the submodules pre-downloaded.

On 12/11/19, Erik Garrison notifications@github.com wrote:

Are our releases including tarballs?

On Tue, Dec 10, 2019 at 11:42 PM Adam Novak notifications@github.com

wrote:

Hello @steinbrl https://github.com/steinbrl

I just did a git clone git://sourceware.org/git/elfutils.git and it

seemed to work. Maybe Sourceware was down, or the git part of it was dfown,

but it came back up? What happens if you rm -Rf deps/elfutils and git

submodule update --init --recursive?

If that still doesn't work, and you can still get to Sourceware's web

pages, what happens if you go to some other folder and try to git clone

--verbose git://sourceware.org/git/elfutils.git? Does it give any more

information on why it can't clone the repo beyond just that it failed?

(Like a complaint that you are out of disk space or something?)

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steinbrl commented 4 years ago

Hi, I tried the recommended tar-ball. The building process failed with this Message:

make[1]: Entering directory '/home/lars/Desktop/NGS/vg_1/vg-v1.20.0/deps/snappy' /bin/bash ./libtool --tag=CXX --mode=compile /usr/bin/g++ -DHAVE_CONFIG_H -I. -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /home/lars/Desktop/NGS/vg_1/vg-v1.20.0/include -I/home/lars/Desktop/NGS/vg_1/vg-v1.20.0/include/dynamic -msse4.2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c -o snappy.lo snappy.cc libtool: Version mismatch error. This is libtool 2.4.2, but the libtool: definition of this LT_INIT comes from libtool 2.4.6. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 libtool: and run autoconf again. Makefile:720: recipe for target 'snappy.lo' failed make[1]: [snappy.lo] Error 63 make[1]: Leaving directory '/home/lars/Desktop/NGS/vg_1/vg-v1.20.0/deps/snappy' Makefile:393: recipe for target 'lib/libsnappy.a' failed make: [lib/libsnappy.a] Error 2

I downloaded now the binary...Thank you !

adamnovak commented 4 years ago

Sounds like maybe vg's build process needs to delete aclocal.m4 from Snappy before building it, because they ship a version that works with exactly one specific version of libtool.

ekg commented 4 years ago

Do we need snappy? We should probably get rid of it.

We aren't building rocksdb anymore are we? That'd be good to axe too.

On Thu, Dec 19, 2019, 19:08 Adam Novak notifications@github.com wrote:

Sounds like maybe vg's build process needs to delete aclocal.m4 http://sushihangover.github.io/mono-libtool-version-mismatch-error-this-is-libtool-2-dot-4-6/ from Snappy before building it, because they ship a version that works with exactly one specific version of libtool.

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adamnovak commented 4 years ago

We are indeed still building RocksDB. I don't think we need it for any real workflows we care about anymore, but nobody has done the work of ripping it out.