Trinity installation issue "/usr/bin/ld: cannot find -ltinfo"

Joanna Kelley

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Jan 30, 2016, 12:03:52 PM1/30/16

to trinityrnaseq-users

Good morning,

I'm trying to install version 2.1.1 and I'm coming up with the following error. I cannot find a way around it and I cannot fix it. If I go into samtools and make it, it will make but doesn't solve the issue. Because there's a trinity_essentials error, Trinity does not run.

Thanks,
Joanna

gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -ltinfo -lcurses -lm -lz -lpthread
/usr/bin/ld: cannot find -ltinfo
collect2: ld returned 1 exit status
make[3]: *** [samtools] Error 1
make[3]: Leaving directory `/home/genomics/tools/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'
make[2]: *** [all-recur] Error 1
make[2]: Leaving directory `/home/genomics/tools/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'
make[1]: *** [samtools] Error 2
make[1]: Leaving directory `/home/genomics/tools/trinityrnaseq-2.1.1/trinity-plugins'
make: *** [trinity_essentials] Error 2

Tiago Hori

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Jan 30, 2016, 12:25:56 PM1/30/16

to Joanna Kelley, trinityrnaseq-users

What are you running this on? You are missing a library necessary of correct compilation using the ncurses library.

If you are using Ubuntu:

sudo apt-get install libtinfo-dev should solve it.

Should solve it.

T.

"Profanity the is the only language all programmers understand"

Sent from my iPhone, the universal excuse for my poor spelling.

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Brian Haas

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Jan 30, 2016, 3:00:49 PM1/30/16

to Tiago Hori, Joanna Kelley, trinityrnaseq-users

Hi Joanna,

Try updating the trinity-plugins/Makefile and commenting out the part w/ LIBPATH as below

cd samtools-0.1.19 && $(MAKE) #LIBPATH=-ltinfo

and see if that helps.

We'll update the makefile to better handle this in the next release, as it's needed on some systems and not others

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

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