[carcalas]

I had no errors during installation. The file libboost_thread.dylib is in:

desktop/boost_1_44_0/stage/lib

I can also find a file with the same name but in other location:

desktop/boost_1_44_0/binV.2/libs_/thread/build/darwin-4.0.1/release/architecture-combined/threading-multi

Any problem with this?

[maubp]

I see now: Having reread your post, you never actually installed the boost library (just built it - i.e. compiled it). You could try pointing MIRA at this folder...

Or, you could try installing BOOST under your home directory (you won't need root access this way):

cd ~/desktop/boost_1_42_0
./bjam install --prefix=/Users/$USER

cd ~/where-ever-you-put-it/mira-3.2.0
./configure --with-boost=/Users/$USER
make
make check

[carcalas]

Ok. Many thanks, maubp. A silly question. When you say users and $User is just it, or I have to indicate a specifc name of the user in both sites. May be it is something obvious for you, but not for me. I will try it and contact you again when finished installing, if you have no troubles.

[maubp]

At the Unix/Linux command line $XXX is shorthand for insert the environment variable XXX here. On Windows you'd use %XXX% instead. Try this:

echo $USER
echo $PATH
echo $HOME

Notice these are case sensitive! It is $USER not $User for example.

With hindsight, using $HOME would have been more elegant.

[carcalas]

Sorry maubp, but I did not understand your last reply. My knowledge of unix is very poor. I am currently following your instructions, compiling boost with the following:

./bjam install --prefix=/Users/$USER

It is running, and seems to be OK. Once finished, I will try to configure mira again typing:

./configure --with-boost=/Users/$USER

Do you think it should work?. Thanks a lot for your patience.

[maubp]

I was trying to explain that this:

./bjam install --prefix=/Users/$USER

should be equivalent to this (assuming your Mac username is carcalas):

./bjam install --prefix=/Users/carcalas

or indeed this:

./bjam install --prefix=$HOME

Hopefully this time MIRA will find BOOST. Fingers crossed

[carcalas]

Hi again, maubp,
The problem with the thread library is solved. But I have now the following error at the end of this sentences:

checking for flex version compatible with MIRA... yes
checking for purify... no
checking whether linking with tcmalloc works... no
checking whether mira should compile in public quiet mode... yes
checking whether mira should compile a development version... yes
checking whether mira should compile with bound tracking... yes
checking whether mira should compile with bug tracking... yes
checking whether mira should compile with extended bug tracking... no
checking whether mira should compile with function trace... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/stdinc/Makefile
config.status: creating src/lec/Makefile
config.status: creating src/errorhandling/Makefile
config.status: creating src/util/Makefile
config.status: creating src/io/Makefile
config.status: creating src/mira/Makefile
config.status: creating src/EdIt/Makefile
config.status: creating src/caf/Makefile
config.status: creating src/examine/Makefile
config.status: creating src/knn_abi373/Makefile
config.status: creating src/knn_alf/Makefile
config.status: creating src/support/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/test/Makefile
config.status: creating src/test/io/Makefile
config.status: creating src/test/io/scf/Makefile
config.status: creating src/test/io/fasta/Makefile
config.status: creating src/test/io/generalio/Makefile
config.status: error: cannot find input file: src/test/mira/Makefile.in

Do you know where is now the problem?

[carcalas]

Hi maubp,
It seem I have solved the last problem. I found the folder mira with the makefile.in not in src/test but in src/mira/mira. I duplicate the folder and put a copy in src/test, and I obtained the following:

config.status: creating src/test/io/Makefile
config.status: creating src/test/io/scf/Makefile
config.status: creating src/test/io/fasta/Makefile
config.status: creating src/test/io/generalio/Makefile
config.status: creating src/test/mira/Makefile
config.status: creating src/test/mira/align/Makefile
config.status: creating src/test/mira/read/Makefile
config.status: creating src/test/mira/readpool/Makefile
config.status: creating src/examples_programming/Makefile
config.status: creating src/progs/Makefile
config.status: creating doc/Makefile
config.status: creating doc/docbook/Makefile
config.status: creating distribution/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands

--------------------------------------------------------------------------------
Summary of MIRA configuration
--------------------------------------------------------------------------------

Could not find the tcmalloc library. It is part of the Google perftools library at

http://code.google.com/p/google-perftools/downloads/list

Please consult the INSTALL file of MIRA for more help on installing it.

Linking to this library is *HIGHLY* recommended as without this library the memory
requirements for MIRA may be 100% higher!

Building version ................................. 3.2.0rc2_dev_darwin9.8.0_i386_32_dynamic
-n Production or development version?................
development

We are building on ............................... Darwin
CPU supports 64 bit? ......... ................... no
Compiler ......................................... gcc
-n Compiler optimisation flags used .................
-O2
Building completely static? ...................... no
-n BOOST expected to compile and link?...............
yes
Linking with TCmalloc library?.................... no

Can MIRA be built on this system? ................ yes (when correctly configured)

This system has been reported as having problems.
Please help fixing if you can.


Using CFLAGS : -O2
Using CXXFLAGS : -DPUBLICQUIET -O2 -pthread -I/Users/cinfante/include
Using LDFLAGS : -L/usr/lib -L/Users/cinfante/lib -lboost_thread

System: Darwin MacBetis.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
Compiler: 'gcc -v' output:
Using built-in specs.
Target: i686-apple-darwin9
Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
Thread model: posix
gcc version 4.0.1 (Apple Inc. build 5493)


--------------------------------------------------------------------------------
Ooops, we might encounter some problems in compilation/linking. Please give
it a try and report success or failure.

Type 'make' to make the binaries and if no error occured,
then 'make install' to install them.

In case of failure, please help to fix if you can.

I think that configure is now OK (Do you think the same?), but the question about tcmalloc library seems to be important. I need some help about this issue.

I tried make, but some errors ocurred and thus I could not execute make install. The errors are:

make[2]: *** [exp_flexer.flex.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

Some ideas, PLEASE?

[maubp]

...
We are building on ............................... Darwin
CPU supports 64 bit? ......... ................... no
...
Linking with TCmalloc library?.................... no
...
I think that configure is now OK (Do you think the same?), but the question about tcmalloc library seems to be important. I need some help about this issue.

Is your Mac really just a 32bit machine? If it is, fine, but if not this will attempt to build a 32bit version of MIRA which will be limited to 4GB of RAM (enough for viruses and maybe easy bacteria).

The TCmalloc thing is an optional library you can use that should reduce the memory used by MIRA a little. Without it, MIRA will use the default malloc for allocating memory. This shouldn't be a problem, and I wouldn't worry about it unless you are running out of RAM during assemblies.

[carcalas]

OK maubp. I suppose my mac is a 32 bit computer; is this issue automatically detected?. I have only 1 Mb of RAM. Do you think MIRA is going to work?.

What is your opinion about the errors detected by the system when executing "make", that is:

make[2]: *** [exp_flexer.flex.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

Thanks again.

[maubp]

OK maubp. I suppose my mac is a 32 bit computer; is this issue automatically detected?.

It should be detected automatically, but this doesn't always work.

I have only 1 Mb of RAM. Do you think MIRA is going to work?.

If you really have 1 megabyte, no way

Even if you have just 1 gigabyte, you will have great trouble running MIRA (expect for the tiniest of assemblies - you may be OK with viral genomes).

To even guess at the memory needed we'd need to know things like what kind of organism are you working on, and what kind of sequencing data, estimated genome size and level of coverage.

What is your opinion about the errors detected by the system when executing "make", that is:

make[2]: *** [exp_flexer.flex.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

Probably what you did with the makefile was wrong. I'd ask on the MIRA mailing list about this.

[carcalas]

Thanks a lot, maubp. Of course, RAM is 1 Gb and not 1 Mb. Sorry for the mistake. I will perform easy analysis, related with virus, with 454 sequences.
I will wait for your ideas about errors while executing "make". Many thanks again.

[maubp]

I've realised you are trying to use the second release candidate, MIRA-3.2.0rc2, when the final release is already out: mira-3.2.0.tar.bz2 is newer than mira-3.2.0rc2.tar.bz2

You may be OK doing 454 assembly of your viruses... but I would plan to get more RAM if I was you.

[carcalas]

Hi Maubp,
I have read the content of the makefile.in, makefile and makefile.am of the mira folder I duplicated and located in the expected direction (src/test/mira), and is exactly the same of the same files located at src/test/mira in a computer of a friend of mine in which mira works. An the content of both mira folders also includes, in addition to the three previous files, three folders named align, read and readpool. So, may be this action was OK, what do you think?.
I will be very grateful to you with any possible solutions to my problems.

[maubp]

I suggest you ask on the MIRA mailing list.