Question: Installing Vicuna on Biolinux 8 - ncbi_tools++ make error
1
gravatar for flacchy
22 months ago by
flacchy40
flacchy40 wrote:

Hi everyone,

we have a new Biolinux system in the lab (Biolinux 8 which is  Ubuntu Linux 14.04 LTS base) and I am struggling to install the program Vicuna (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna). I am wondering if anyone could help me to sort it out. I think the major problem is the dependency from ncbi_tools++.

I have followed the installation for external users and downloaded the NCBI toolkit from the ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT, then configured it specifying the path, and finally `make` and `make install`.

The problem is that every time I am trying to run ‘make’ after the configuration of the ncbi_tools++ I get various make errors. And if I try to ignore these errors and install vicuna, the program will not run (I just gave it a try anyway).

I have tried to install the program both in bash and zsh environments as well as installing it in different locatoions without much luck.

I know Biolinux have already a version of the ncbi_tools

> ncbi-tools-x11                6.1.20120620      NCBI libraries for biology applications (X-based utilities)

But I am not sure if this is creating conflict with what I am trying to install.

If anyone could help me it would be much appreciated.

Any advice will be welcome

 

Regards

F. 

ADD COMMENTlink modified 21 months ago • written 22 months ago by flacchy40

What are the errors from make?

ADD REPLYlink written 22 months ago by george.ry1.0k

let's put on the magic hat and see if we can guess what the problem is without seeing the errors...

 

If make works, but make install doesn't, then very likely it's a permissions problem.

The other common issue is missing headers.

 

That's about as far as the crystal ball with take us. If you post the errors from make, this should get a lot easier :)

ADD REPLYlink written 22 months ago by bbecker30

collect2: error: ld returned 1 exit status
make[5]: *** [ace2asn] Error 1
make[5]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app'
FAILED: src/objtools/readers/app/Makefile.ace2asn.app
make[5]: Entering directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app'
/bin/rm -f ace2asn .ace2asn.stamp
make[5]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app'
make[4]: *** [all.nonusr] Error 2
make[4]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app'
make[3]: *** [all_r.real] Error 5
make[3]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers'
make[2]: *** [all_r.real] Error 5
make[2]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools'
make[1]: *** [all_r.real] Error 5
make[1]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build'
make: *** [all] Error 2

ADD REPLYlink modified 22 months ago • written 22 months ago by flacchy40

ok :

 

collect2: error: ld returned 1 exit status

that's a linker error, which means you can't find some dependent library. The thing that needs the library is ace2asn, but  the other stuff is not useful, we need to see the Error 1's before that.

CAN HAZ MOAR LOG !!!???

ADD REPLYlink written 22 months ago by bbecker30

thanks .. that's actually make sense . is there an easy way to have the errors as a text file instead of the screen?

ADD REPLYlink written 22 months ago by flacchy40
1

Try

make 2> errors.txt 

for just the errors, or 

make &> make_output.txt

to capture everything. If you want the screen pollution too you can use tee

make | tee make_outptut.txt
ADD REPLYlink written 22 months ago by gordon.wells30

looks like you just have to paste the relevant bits, no matter how large they are. The other option is to use pastebin or a github gist or something like that.

ADD REPLYlink written 22 months ago by bbecker30

Apology it took forever but I was not able to save the output. Anyway here is ERROR 1:

% sudo make [ 1:04PM] if test -f /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/Makefile.flat; then \ cd /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build && make -f Makefile.flat; \ elif test -s ""; then \ cd /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build && make all_p; \ else \ cd /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build && make all_r; \ fi make[1]: Entering directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build' make[1]: [/home/Programs/ncbi_cxx--12_0_0/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/home/Programs/ncbi_cxx--12_0_0/src/gui/Makefile.in] Error 1 (ignored)

it's the same when I try to install the program in usr/local

ADD REPLYlink written 21 months ago by flacchy40

I've manage to remove one error by running

sudo -i

make

but now I am getting this:

=======================================

collect2: error: ld returned 1 exit status make[5]: * [ace2asn] Error 1 make[5]: Leaving directory /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app' FAILED: src/objtools/readers/app/Makefile.ace2asn.app make[5]: Entering directory/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app' /bin/rm -f ace2asn .ace2asn.stamp make[5]: Leaving directory /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app' make[4]: *** [all.nonusr] Error 2 make[4]: Leaving directory/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers/app' make[3]: [all_r.real] Error 5 make[3]: Leaving directory /home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools/readers' make[2]: *** [all_r.real] Error 5 make[2]: Leaving directory/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build/objtools' make[1]: [all_r.real] Error 5 make[1]: Leaving directory `/home/Programs/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/build' make: * [all] Error 2

=======================

any idea on how to solve this?

ADD REPLYlink modified 21 months ago by Istvan Albert ♦♦ 75k • written 21 months ago by flacchy40
3
gravatar for bbecker
22 months ago by
bbecker30
bbecker30 wrote:

let's put on the magic hat and see if we can guess what the problem is without seeing the errors...

 

If make works, but make install doesn't, then very likely it's a permissions problem.

The other common issue is missing headers.

 

That's about as far as the crystal ball with take us. If you post the errors from make, this should get a lot easier :)

ADD COMMENTlink written 22 months ago by bbecker30
1

Re -running it so I can post the errors, apology for not thinking about that before! will post it asap 

ADD REPLYlink written 22 months ago by flacchy40

this is clearly not an answer, sorry  - it was a comment :)

ADD REPLYlink written 22 months ago by bbecker30
1
gravatar for flacchy
21 months ago by
flacchy40
flacchy40 wrote:

SOLVE IT!

Thanks to Tim Carr of eResearch UCT.

when configuring the Ncbi-tools remove the --with-dll flag then make and make install run without errors

Hope this can help someone else

F.

ADD COMMENTlink written 21 months ago by flacchy40

Thanks for following up.

ADD REPLYlink written 21 months ago by Istvan Albert ♦♦ 75k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1288 users visited in the last hour