Problem installing Trinity

[Tomás Carrasco]

I try install both trinity 2.3.2 and 2.4.0 and with both I get the same error 

[trinityrnaseq-Trinity-v2.4.0] make

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... a.out

checking whether the C++ compiler works... configure: error: in `/Venus_Apple/programs/trinityrnaseq-Trinity-v2.4.0/Inchwo

configure: error: cannot run C++ compiled programs.

If you meant to cross compile, use `--host'.

See `config.log' for more details.

make: *** [inchworm_target] Error 1

The I think that this is because my g++ but 

[trinityrnaseq-Trinity-v2.4.0] g++ -v

Using built-in specs.

COLLECT_GCC=g++

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.5-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/doc++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdible-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clolibstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plro --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5b/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enabler --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --bui --target=x86_64-linux-gnu

Thread model: posix

gcc version 4.8.5 (Ubuntu 4.8.5-2ubuntu1~14.04.1)

Or maybe build-essential

[trinityrnaseq-Trinity-v2.4.0] sudo apt-get install build-essential

Reading package lists... Done

Building dependency tree

Reading state information... Done

build-essential is already the newest version.

build-essential set to manually installed.

0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

 but nothing work u.u

here what the config.log say, I understand nothing 

This file contains any messages produced by compilers while

running configure, to aid debugging if configure makes a mistake.

It was created by Inchworm configure 0.1, which was

generated by GNU Autoconf 2.63.  Invocation command line was

  $ ./configure --prefix=/Venus_Apple/programs/trinityrnaseq-Trinity-v2.3.2/Inchworm

## --------- ##

## Platform. ##

## --------- ##

hostname = Venus

uname -m = x86_64

uname -r = 3.13.0-113-generic

uname -s = Linux

uname -v = #160-Ubuntu SMP Thu Mar 9 09:27:29 UTC 2017

/usr/bin/uname -p = unknown

/bin/uname -X     = unknown

/bin/arch              = unknown

/usr/bin/arch -k       = unknown

/usr/convex/getsysinfo = unknown

/usr/bin/hostinfo      = unknown

/bin/machine           = unknown

/usr/bin/oslevel       = unknown

/bin/universe          = unknown

PATH: /usr/local/sbin

PATH: /usr/local/bin

PATH: /usr/sbin

PATH: /usr/bin

PATH: /snap/bin

## ----------- ##

## Core tests. ##

## ----------- ##

configure:1831: checking for a BSD-compatible install

configure:1899: result: /usr/bin/install -c

configure:1910: checking whether build environment is sane

configure:1970: result: yes

configure:2111: checking for a thread-safe mkdir -p

configure:2150: result: /bin/mkdir -p

configure:2163: checking for gawk

configure:2179: found /usr/bin/gawk

configure:2190: result: gawk

configure:2201: checking whether make sets $(MAKE)

configure:2223: result: yes

configure:2369: checking for g++

configure:2385: found /usr/bin/g++

configure:2396: result: g++

configure:2423: checking for C++ compiler version

configure:2431: g++ --version >&5

g++ (Ubuntu 4.8.5-2ubuntu1~14.04.1) 4.8.5

Copyright (C) 2015 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2435: $? = 0

configure:2442: g++ -v >&5

Using built-in specs.

COLLECT_GCC=g++

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.5-2ubuntu1~14.04.1' --with-bugurl=file:///usr/share/do$

Thread model: posix

gcc version 4.8.5 (Ubuntu 4.8.5-2ubuntu1~14.04.1)

configure:2446: $? = 0

configure:2453: g++ -V >&5

g++: error: unrecognized command line option '-V'

g++: fatal error: no input files

compilation terminated.

configure:2457: $? = 4

configure:2480: checking for C++ compiler default output file name

configure:2502: g++    conftest.cpp  >&5

configure:2506: $? = 0

configure:2544: result: a.out

configure:2563: checking whether the C++ compiler works

configure:2573: ./a.out

configure:2563: checking whether the C++ compiler works

configure:2573: ./a.out

./configure: line 2575: ./a.out: Permission denied

configure:2577: $? = 126

configure:2584: error: in `/Venus_Apple/programs/trinityrnaseq-Trinity-v2.3.2/Inchworm':

configure:2588: error: cannot run C++ compiled programs.

If you meant to cross compile, use `--host'.

See `config.log' for more details.

## ---------------- ##

## Cache variables. ##

## ---------------- ##

ac_cv_env_CCC_set=

ac_cv_env_CCC_value=

ac_cv_env_CPPFLAGS_set=

ac_cv_env_CPPFLAGS_value=

ac_cv_env_CXXFLAGS_set=

ac_cv_env_CXXFLAGS_value=
and so...

Please help

[Tiago Hori]

I am going to go on a limb here and say that you don’t have the privileges to write on /Venus_Apple/programs/trinityrnaseq-Trinity-v2.3.2/Inchworm

 

Have you tried to install it locally?

 

T.

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

[Tomás Carrasco]

I have tried as sudo but doest'n work eigther

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

[Tiago Hori]

Is this a server or just a local computer? If it is a server, sudo may not help.

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.

To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.

[Tomás Carrasco]

It´'s a server but it's near so I can used a local machine, nevertheless I only tried as ssh, I'll try as local

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

[Tomás Carrasco]

ok now i'm siting in the machine, but is not different

[trinityrnaseq-Trinity-v2.3.2] sudo make                   [11:34]
[sudo] password for claudio:

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... a.out

checking whether the C++ compiler works... configure: error: in `/Venus_Apple/programs/trinityrnaseq-Trinity-v2.3.2/Inchworm':

configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `

--host'.
See `config.log' for more details.

make: *** [inchworm_target] Error 1

claudio@Venus[trinityrnaseq-Trinity-v2.3.2]

[Tomás Carrasco]

I also try a sudo chmod -R 777 . from the ../trinity directory but nothing

[Will Holtz]

> configure:2563: checking whether the C++ compiler works

> configure:2573: ./a.out

> ./configure: line 2575: ./a.out: Permission denied

Looks like you might be lacking write permissions in the directory you are trying to run make in. 

-Will

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

To post to this group, send email to trinityrnaseq-users@googlegroups.com.

Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed.  If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited.  If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).

Please consider the environment before printing this email.

[Horacio Montenegro]

by locally I think he meant install Trinity somewhere on your $HOME
folder - like $HOME/bin/trinity or $HOME/bin/trinity-2.3.2

>>> email to trinityrnaseq-u...@googlegroups.com.

>>> To post to this group, send email to trinityrn...@googlegroups.com.
>>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "trinityrnaseq-users" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an

>>> email to trinityrnaseq-u...@googlegroups.com.

>>> To post to this group, send email to trinityrn...@googlegroups.com.
>>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>>> For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to the Google Groups
> "trinityrnaseq-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an

> email to trinityrnaseq-u...@googlegroups.com.

> To post to this group, send email to trinityrn...@googlegroups.com.
> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
> For more options, visit https://groups.google.com/d/optout.



--

Horácio Montenegro
Laboratório de Biologia Molecular de Plantas
Departamento de Genética
Escola Superior de Agricultura "Luiz de Queiroz"
Avenida Pádua Dias, 11 - Piracicaba - São Paulo - Brasil
CEP: 13418-900