trinity installation error

[Peng Xiao]

I'm new in Linux. When I install Trinity, it showed these errors:

Using gnu compiler for Inchworm and Chrysalis

cd Inchworm && (test -e configure || autoreconf) \

                && sh ./configure --prefix=`pwd`  && make install

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

checking for g++... g++

checking for C++ compiler default output file name... 

configure: error: in `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/Inchworm':

configure: error: C++ compiler cannot create executables

See `config.log' for more details.

make: *** [inchworm_target] Error 77

gcc -v :

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/export/app/gcc-4.9.1/libexec/gcc/x86_64-unknown-linux-gnu/4.9.1/lto-wrapper

Target: x86_64-unknown-linux-gnu

Configured with: ./configure --prefix=/export/app/gcc-4.9.1 -enable-threads=posix -disable-checking -disable-multilib -enable-languages=c --with-gmp=/export/app/gmp-4.3.2 --with-mpfr=/export/app/mpfr-2.4.2 --with-mpc=/export/app/mpc-0.8.1

Thread model: posix

gcc version 4.9.1 (GCC) 

Any help will be appreciated! Thanks a lot!

[Tiago Hori]

Can you find the config.log file and send it to us?

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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[Peng Xiao]

Thanks very much!

I googled and find a solution:

add the lib folders of gmp, mpfr and mpc to the environment variables, while it showed new errors:

ln -sf parafly-code parafly

ln -sf Trimmomatic-0.32 Trimmomatic

tar xvf samtools-0.1.19.tar.bz2

samtools-0.1.19/

samtools-0.1.19/.gitignore

samtools-0.1.19/AUTHORS

samtools-0.1.19/COPYING

samtools-0.1.19/ChangeLog.old

samtools-0.1.19/INSTALL

samtools-0.1.19/Makefile

samtools-0.1.19/Makefile.mingw

samtools-0.1.19/NEWS

samtools-0.1.19/bam.c

samtools-0.1.19/bam.h

samtools-0.1.19/bam2bcf.c

samtools-0.1.19/bam2bcf.h

samtools-0.1.19/bam2bcf_indel.c

samtools-0.1.19/bam2depth.c

samtools-0.1.19/bam_aux.c

samtools-0.1.19/bam_cat.c

samtools-0.1.19/bam_color.c

samtools-0.1.19/bam_endian.h

samtools-0.1.19/bam_import.c

samtools-0.1.19/bam_index.c

samtools-0.1.19/bam_lpileup.c

samtools-0.1.19/bam_mate.c

samtools-0.1.19/bam_md.c

samtools-0.1.19/bam_pileup.c

samtools-0.1.19/bam_plcmd.c

samtools-0.1.19/bam_reheader.c

samtools-0.1.19/bam_rmdup.c

samtools-0.1.19/bam_rmdupse.c

samtools-0.1.19/bam_sort.c

samtools-0.1.19/bam_stat.c

samtools-0.1.19/bam_tview.c

samtools-0.1.19/bam_tview.h

samtools-0.1.19/bam_tview_curses.c

samtools-0.1.19/bam_tview_html.c

samtools-0.1.19/bamshuf.c

samtools-0.1.19/bamtk.c

samtools-0.1.19/bcftools/

samtools-0.1.19/bcftools/Makefile

samtools-0.1.19/bcftools/README

samtools-0.1.19/bcftools/bcf.c

samtools-0.1.19/bcftools/bcf.h

samtools-0.1.19/bcftools/bcf.tex

samtools-0.1.19/bcftools/bcf2qcall.c

samtools-0.1.19/bcftools/bcfutils.c

samtools-0.1.19/bcftools/call1.c

samtools-0.1.19/bcftools/em.c

samtools-0.1.19/bcftools/fet.c

samtools-0.1.19/bcftools/index.c

samtools-0.1.19/bcftools/kfunc.c

samtools-0.1.19/bcftools/kmin.c

samtools-0.1.19/bcftools/kmin.h

samtools-0.1.19/bcftools/main.c

samtools-0.1.19/bcftools/mut.c

samtools-0.1.19/bcftools/prob1.c

samtools-0.1.19/bcftools/prob1.h

samtools-0.1.19/bcftools/vcf.c

samtools-0.1.19/bcftools/vcfutils.pl

samtools-0.1.19/bcftools/bcf.h~

samtools-0.1.19/bedcov.c

samtools-0.1.19/bedidx.c

samtools-0.1.19/bgzf.c

samtools-0.1.19/bgzf.h

samtools-0.1.19/bgzip.c

samtools-0.1.19/cut_target.c

samtools-0.1.19/errmod.c

samtools-0.1.19/errmod.h

samtools-0.1.19/examples/

samtools-0.1.19/examples/00README.txt

samtools-0.1.19/examples/Makefile

samtools-0.1.19/examples/bam2bed.c

samtools-0.1.19/examples/calDepth.c

samtools-0.1.19/examples/chk_indel.c

samtools-0.1.19/examples/ex1.fa

samtools-0.1.19/examples/ex1.sam.gz

samtools-0.1.19/examples/toy.fa

samtools-0.1.19/examples/toy.sam

samtools-0.1.19/faidx.c

samtools-0.1.19/faidx.h

samtools-0.1.19/kaln.c

samtools-0.1.19/kaln.h

samtools-0.1.19/khash.h

samtools-0.1.19/klist.h

samtools-0.1.19/knetfile.c

samtools-0.1.19/knetfile.h

samtools-0.1.19/kprobaln.c

samtools-0.1.19/kprobaln.h

samtools-0.1.19/kseq.h

samtools-0.1.19/ksort.h

samtools-0.1.19/kstring.c

samtools-0.1.19/kstring.h

samtools-0.1.19/misc/

samtools-0.1.19/misc/HmmGlocal.java

samtools-0.1.19/misc/Makefile

samtools-0.1.19/misc/ace2sam.c

samtools-0.1.19/misc/bamcheck.c

samtools-0.1.19/misc/blast2sam.pl

samtools-0.1.19/misc/bowtie2sam.pl

samtools-0.1.19/misc/export2sam.pl

samtools-0.1.19/misc/interpolate_sam.pl

samtools-0.1.19/misc/maq2sam.c

samtools-0.1.19/misc/md5.c

samtools-0.1.19/misc/md5.h

samtools-0.1.19/misc/md5fa.c

samtools-0.1.19/misc/novo2sam.pl

samtools-0.1.19/misc/plot-bamcheck

samtools-0.1.19/misc/psl2sam.pl

samtools-0.1.19/misc/r2plot.lua

samtools-0.1.19/misc/sam2vcf.pl

samtools-0.1.19/misc/samtools.pl

samtools-0.1.19/misc/soap2sam.pl

samtools-0.1.19/misc/varfilter.py

samtools-0.1.19/misc/vcfutils.lua

samtools-0.1.19/misc/wgsim.c

samtools-0.1.19/misc/wgsim_eval.pl

samtools-0.1.19/misc/zoom2sam.pl

samtools-0.1.19/padding.c

samtools-0.1.19/phase.c

samtools-0.1.19/razf.c

samtools-0.1.19/razf.h

samtools-0.1.19/razip.c

samtools-0.1.19/sam.c

samtools-0.1.19/sam.h

samtools-0.1.19/sam_header.c

samtools-0.1.19/sam_header.h

samtools-0.1.19/sam_view.c

samtools-0.1.19/sample.c

samtools-0.1.19/sample.h

samtools-0.1.19/samtools.1

samtools-0.1.19/win32/

samtools-0.1.19/win32/libcurses.a

samtools-0.1.19/win32/libz.a

samtools-0.1.19/win32/xcurses.h

samtools-0.1.19/win32/zconf.h

samtools-0.1.19/win32/zlib.h

samtools-0.1.19/bam.h~

cd samtools-0.1.19 && make LIBPATH=-ltinfo

make[2]: Entering directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[3]: Entering directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[4]: Entering directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[4]: Nothing to be done for `lib'.

make[4]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[4]: Entering directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19/bcftools'

make[4]: Nothing to be done for `lib'.

make[4]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19/bcftools'

make[4]: Entering directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19/misc'

make[4]: Nothing to be done for `lib'.

make[4]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19/misc'

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: error: ld returned 1 exit status

make[3]: *** [samtools] Error 1

make[3]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[2]: *** [all-recur] Error 1

make[2]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins/samtools-0.1.19'

make[1]: *** [samtools] Error 2

make[1]: Leaving directory `/data2/xiaopeng/xp/trinity/trinityrnaseq-2.1.1/trinity-plugins'

make: *** [trinity_essentials] Error 2

I tried to install some package which contains the libtinfo.so, but failed. I didn't have the root rights, could you please give me some advice?

Thanks very much!

Best Wishes,

Peng

在 2015年12月15日星期二 UTC+8下午6:55:32，Tiago Hori写道：

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[Xiao Peng]

I also tried this:

cd trinity-plugins/samtools-0.1.19/ && make  #delete the code 'LIBPATH=-ltinfo'

and it showed no error, but i don't what's the difference. is it ok to just delete that code?

Thanks very much for your kindly help!

Best wishes,

Peng

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Shenzhen Key Laboratory of Marine Biological Resources

and Ecological Environment

College of Life Sciences, Shenzhen University

518060, Shenzhen, China

E-mail: goog...@gmail.com

Tel: +86 15827609557

[Tiago Hori]

My guess is that you need to install the ncurses library, but if you don't have super user privileges, you may need to ask you system admin to do it.

T.

"Profanity the is the only language all programmers understand" 

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

[Peng Xiao]

Thanks very much!

I will ask the IT for help!

Thank you!

Best,

Peng

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--

Shenzhen Key Laboratory of Marine Biological Resources

and Ecological Environment

College of Life Sciences, Shenzhen University

518060, Shenzhen, China

E-mail: goog...@gmail.com

Tel: +86 15827609557

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