Question

Installing Vicuna on Biolinux 8 - ncbi_tools++ make error

1

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8.7 years ago

flacchy ▴ 40

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. 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, 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.

Assembly vicuna biolinux denovo next-gen • 4.4k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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What are the errors from make?

ADD REPLY • link 8.7 years ago by george.ry ★ 1.2k

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by bbecker ▴ 30

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by bbecker ▴ 30

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

ADD REPLY • link 8.7 years ago by flacchy ▴ 40

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by gordon.wells ▴ 30

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by bbecker ▴ 30

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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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 REPLY • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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8.7 years ago

flacchy ▴ 40

SOLVED 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 COMMENT • link updated 2.3 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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Thanks for following up.

ADD REPLY • link 8.7 years ago by Istvan Albert 101k

Ram · Accepted Answer · 2016-02-19

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8.7 years ago

bbecker ▴ 30

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 COMMENT • link updated 6.1 years ago by Ram 44k • written 8.7 years ago by bbecker ▴ 30

1

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

ADD REPLY • link updated 2.3 years ago by Ram 44k • written 8.7 years ago by flacchy ▴ 40

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

ADD REPLY • link updated 2.3 years ago by Ram 44k • written 8.7 years ago by bbecker ▴ 30