search

FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
111 stars 17 forks source link

Trouble installing in Ubuntu 18.04; error with libnlopt-cxx-dev #107

Closed drelo closed 5 years ago

drelo commented 5 years ago

Hi, maybe this is a minor thing but I am installing phyx in a new machine, with Ubuntu 18.04. First I got the error

E: Unable to locate package libnlopt-cxx-dev I don't know if this is available in 18.04 but maybe I am doing something wrong [This machine in the lab should stay under LTS].

I proceeded with the install anyway and I got errors during the run_tests.py step. How could I fix this? Thanks

josephwb commented 5 years ago

Did you follow these instructions? It includes installation of the nlopt dependency.

What is the error from run_tests.py?

drelo commented 5 years ago

I followed those instructions now. It returned errors. I saved them in this file. problem.txt

josephwb commented 5 years ago

Hmm I am getting these same errors myself now. Will check on it. Thanks for the issue.

As for nlopt, what happens when you do:

 sudo apt-get install git autotools-dev autoconf automake cmake libtool liblapack-dev libatlas-cpp-0.6-dev libnlopt-dev libnlopt0
josephwb commented 5 years ago

As to the errors, it looks like a test input has changed, so the tests do not match the expected results. Will fix soon.

josephwb commented 5 years ago

Ok all but 1 are now passing. Do git pull, and recompile.

josephwb commented 5 years ago

And the last now works. Sorry about that. Let's make sure your installation works now. Please run the apt-get command above and let us know what you get.

drelo commented 5 years ago

that line seems to work fine

autoconf is already the newest version (2.69-11). automake is already the newest version (1:1.15.1-3ubuntu2). autotools-dev is already the newest version (20180224.1). liblapack-dev is already the newest version (3.7.1-4ubuntu1). libtool is already the newest version (2.4.6-2). libatlas-cpp-0.6-dev is already the newest version (0.6.3-4ubuntu1). libnlopt-dev is already the newest version (2.4.2+dfsg-4). libnlopt0 is already the newest version (2.4.2+dfsg-4). cmake is already the newest version (3.10.2-1ubuntu2.18.04.1). git is already the newest version (1:2.17.1-1ubuntu0.4).

El jue., 12 sept. 2019 a las 19:37, Joseph W. Brown (< notifications@github.com>) escribió:

Hmm I am getting these same errors myself now. Will check on it. Thanks for the issue.

As for nlopt, what happens when you do:

sudo apt-get install git autotools-dev autoconf automake cmake libtool liblapack-dev libatlas-cpp-0.6-dev libnlopt-dev libnlopt0

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/107?email_source=notifications&email_token=ACO2NCSOI6I5IHW3YOXBWODQJLACZA5CNFSM4IWJHM62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6TOYSA#issuecomment-531033160, or mute the thread https://github.com/notifications/unsubscribe-auth/ACO2NCT5J62LBORM3SOTPPTQJLACZANCNFSM4IWJHM6Q .

josephwb commented 5 years ago

Hmm. Ok try:

git pull
make distclean
autoreconf -fi
./configure
make

configure should have a output like:

checking for nlopt_version in -lnlopt... yes
drelo commented 5 years ago

Sorry I just arrived here and I finished checking this. 41 passed. Everything is fine. Thanks for the quick response. Should I close this?

Selection_017

josephwb commented 5 years ago

Thanks again for raising this. Are you still getting an nlopt error?

drelo commented 5 years ago

No problem with that now, the only line giving problems was sudo apt install libnlopt-cxx-dev and it is fixed now.

El jue., 12 sept. 2019 a las 20:31, Joseph W. Brown (< notifications@github.com>) escribió:

Thanks again for raising this. Are you still getting an nlopt error?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/107?email_source=notifications&email_token=ACO2NCTEEGH4OB33CBNXVQ3QJLGMZA5CNFSM4IWJHM62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6TRS6I#issuecomment-531044729, or mute the thread https://github.com/notifications/unsubscribe-auth/ACO2NCSANK3FYI3EEXWYT6TQJLGMZANCNFSM4IWJHM6Q .

drelo commented 5 years ago

Did you follow these instructions? It includes installation of the nlopt dependency.

@josephwb , the main page https://github.com/FePhyFoFum/phyx still has the problematic instructions to install cxxx-dev, I just noticed this because in another machine at the lab I left that tab open and started to install/build from there.

josephwb commented 5 years ago

Hmm I actually do not know if we need libnlopt-cxx-dev. Do you @blackrim?

blackrim commented 5 years ago

It uses it for optimization I believe still.

On Fri, Sep 13, 2019 at 2:30 PM Joseph W. Brown notifications@github.com wrote:

Hmm I actually do not know if we need libnlopt-cxx-dev. Do you @blackrim https://github.com/blackrim?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/FePhyFoFum/phyx/issues/107?email_source=notifications&email_token=AABHGKL6FEPV3OUOBOGPHCDQJPL5XA5CNFSM4IWJHM62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6V2YII#issuecomment-531344417, or mute the thread https://github.com/notifications/unsubscribe-auth/AABHGKOVYEURIL6MZOG6VUDQJPL5XANCNFSM4IWJHM6Q .

josephwb commented 5 years ago

Hrm ok my apt-get (Ubuntu 18) does not even have that package or anything similar.

Cactusolo commented 4 years ago

Hi, just follow up, I have the same issue, before I git clone phy repo:

~/apps$ sudo apt install libnlopt-cxx-dev Reading package lists... Done Building dependency tree
Reading state information... Done E: Unable to locate package libnlopt-cxx-dev

I also tried suggestions from here

But no luck.

Thanks!

I am running Operating System: Ubuntu 18.04.3 LTS

josephwb commented 4 years ago

I have not been able to find libnlopt-cxx-dev. Trusn out you don't need it anyway. Omit that dependency, then do:

./configure
make
make check

to confirm things work. If so, please report here, and I will just take that dependency out of the docs.

Cactusolo commented 4 years ago

@josephwb Yeah, you are right, we don't need libnlopt-cxx-dev so far as I tell. I went down all those steps and has phyx successfully working everywhere in my system.
Thanks!

josephwb commented 4 years ago

Thanks. It is gone.