[mira_talk] Re: Help with the Mira 3.9.16 installation with Boost library on Mac osx
- From: Austen Chen <austen.chen@xxxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 15 May 2013 12:57:50 +0000
Thank you so much Sebastian that MIRA configuration worked using
--with-librries=all (see below). However I ran into another problem after
hitting 'make'. As Bastien pointed out:
Please note: at the moment I cannot guarantee that MIRA will work on OSX.
There is an obscure bug which strikes under some circumstances, but I
currently have no possibility to hunt for it it seems to strike only
larger projects (for which I am lacking the necessary RAM under OSX).
To be more precise: I discourage using MIRA under OSX for anything but
small projects with a few thousand reads.
It's beyond me now and should I call it quits? Or can it be a piece of
useful information for you guys if you are interested?
It would be good at least to be able to have MIRA installed on OSX if it's
not too much trouble.
Still many thanks for all the help
Summary of MIRA configuration
---------------------------------------------------------------------------
-----
Linking against tcmalloc is disabled!
Note that this is the default for OS X, but you might want to try switching
it on like this: --with-tcmalloc
Building version .................................
3.9.16_darwin12.3.0_x86_64_dynamic
We are building on ............................... Darwin
CPU supports 64 bit? ............................. yes
Compiler ......................................... gcc
Compiler optimisation flags used ................. -O3 -funroll-loops
Do we compile in 64 bit? ......................... yes
Building completely static? ...................... no
BOOST expected to compile and link? .............. yes
Linking with TCmalloc library? ................... no
Can MIRA be built on this system? ................ yes
Using CFLAGS : -mmacosx-version-min=10.5 -O3 -funroll-loops
-I/usr/include -Werror=uninitialized -Werror=return-type
Using CXXFLAGS : -DPUBLICQUIET -mmacosx-version-min=10.5 -O3
-funroll-loops -pthread -I/Users/145034/include -I/usr/include
-Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x
-Werror=unused-value
Using LDFLAGS : -Wl,-no_compact_unwind -L/Users/a1180171/lib -L/usr/lib
Using LIBS : -lboost_thread -lboost_regex -lboost_system
-lboost_filesystem -lboost_iostreams -lexpat -lm -lz -lbz2
Looks good, we do not expect compilation problems.
---------------------------------------------------------------------------
-----
Type 'make' to make the binaries
and then 'make install' to install them.
$ make
make all-recursive
Making all in src
make all-recursive
Making all in debuggersupport
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"3.9.16\" -DPACKAGE_STRING=\"mira\ 3.9.16\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"3.9.16\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1
-DHAVE_STRFTIME=1 -DHAVE_FLOOR=1 -DHAVE_MEMSET=1 -DHAVE_POW=1
-DHAVE_SQRT=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/
-DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/
-DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/
-DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/
-DHAVE_BOOST_IOSTREAMS=/\*\*/ -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.
-I../../src -DPUBLICQUIET -mmacosx-version-min=10.5 -O3
-funroll-loops -pthread -I/Users/145034/include -I/usr/include
-Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x
-Werror=unused-value -MT dbgsupport.o -MD -MP -MF .deps/dbgsupport.Tpo -c
-o dbgsupport.o dbgsupport.C
cc1plus: error: unrecognized command line option "-std=c++0x"
make[4]: *** [dbgsupport.o] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
On 15/05/13 6:14 PM, "Sebastian Juenemann"
<jueneman@xxxxxxxxxxxxxxxxxxxxxxxx> wrote:
>On 05/15/13 08:49, Austen Chen wrote:
>> Thank you Sebastian for your help. I should have added more detailed
>> information in my first email.
>>
>> What happened was that if I did this: ./bootstrap.sh
>> --with-libraries=thread,regex,system
>>
>> I got this error during MIRA configure script:
>>
>> checking whether the Boost::Filesystem library is available... yes
>> configure: error: Could not link against boost_system !
>>
>>
>> But if I did this:./bootstrap.sh --with-libraries=thread,regex, system,
>> filesystem
>>
>> Then I got the following:
>>
>> checking whether the Boost::System library is available... yes
>> checking for exit in -lboost_system... Yes
>>
>>
>> checking whether the Boost::Filesystem library is available... yes
>> checking for exit in -lboost_filesystem... Yes
>>
>>
>> checking whether the Boost::IOStreams library is available... yes
>> configure: error: Could not link against boost_filesystem !
>>
>> I could be wrong but it looks like that MIRA had no problem locating the
>> boost_system if I added filesystem, and then something else became the
>> problem (in this case the Boost::IOStreams library). It seems like that
>>I
>> need to keep adding more and moreŠthat's why I stopped and thought that
>> there must be a more concise way of doing it. Or to make it simply
>>should
>> I install the complete boost library on my computer first? Any help on
>> this?
>
>Really looks like your boost is not compete. Of course it would be
>helpful if you can check whether you have the most recent version of
>BOOST installed on your system and if it's installed complete or not.
>Also, why not using just:
>
>./bootstrap.sh --with-libraries=all ?
>
>If you still have problems locating the boost libs than you should try
>further and point to the boost location via './configure --with-boost= '
>and '--with-boost-libdir='
>
>
>>
>> Thanks
>>
>> Aus
>>
>> On 15/05/13 12:12 AM, "Sebastian Juenemann"
>> <jueneman@xxxxxxxxxxxxxxxxxxxxxxxx> wrote:
>>
>>> On 05/14/13 15:47, Austen Chen wrote:
>>>> Dear all,
>>>>
>>>> I was trying to install Mira 3.9.16 on my Mac osx 10.8.3. Then I
>>>> realised that I also needed to install the Boost library. After
>>>> searching on the MIRA_talk I found the following instructions (see
>>>> below) and I was following that instructions using the latest version
>>>>of
>>>> boost_1_53_0. however i was getting this error from the MIRA configure
>>>> script:
>>>>
>>>> checking whether the Boost::Filesystem library is available... yes
>>>> configure: error: Could not link against boost_system !
>>>>
>>>> I then added system to
>>>> ./bootstrap.sh --with-libraries=thread,regex, system
>>>>
>>>> but still got the same error.
>>>>
>>>> I then added filesystem to
>>>> ./bootstrap.sh --with-libraries=thread,regex, system, filesystem
>>>>
>>>> But still could not get it to work. Maybe Mira 3.9.16 requires more
>>>> components installed? But how many more?
>>>
>>> Austen - this does not help as you're already linking against these
>>> libraries. What MIRA does say here is that it can not _find_ them, i.e.
>>> the boost_system lib can't be found but is (explicit) required
>>> (--with-libraries=...). Were there normally installed on your system,
>>>as
>>> boost::filesystem could be found? What may help:
>>>
>>> ./configure --help
>>>
>>> You can try to provide an additional parameter for configure to _find_
>>> your required boost library, i.e.:
>>>
>>> --with-boost-libdir=[path to boost]
>>>
>>> If this does not help, as e.g. they are located at different
>>> directories, you can try to export the CFLAGS/CXXFLAGS and LDFLAGS
>>> environmental variables pointing to desired include and lib
>>>directories,
>>> respectively.
>>>
>>> If you have system or compiler special boost libs, you need to tell the
>>> linker to use those instead of the default ones by providing these
>>> information via './configure --with-boost-system=[library]'.
>>>
>>> I hope this helps,
>>>
>>> - Sebastian
>>>
>>>>
>>>> I was wondering if anyone could update the instructions of the boost
>>>> library for this latest version of MIRA?
>>>>
>>>> Thank you so much in advance
>>>>
>>>> Aus
>>>>
>>>> (02-15-2011) Just a note for anyone using my instructions above,
>>>>they've
>>>> been fine for me up to and including MIRA 3.2.0.
>>>>
>>>> As of MIRA 3.2.1 you'll also need the BOOST regex library - I was
>>>> getting this error from the MIRA configure script:
>>>> Code:
>>>>
>>>> checking whether the Boost::Regex library is available... yes
>>>> configure: error: Could not link against boost_thread !
>>>>
>>>> So, install BOOST again (I tried with BOOST 1.42.0 initially since I
>>>> already had that, then again with the latest release, BOOST 1.45.0)
>>>>but
>>>> with regex this time:
>>>> Code:
>>>>
>>>> cd boost_1_45_0
>>>> ./bootstrap.sh --with-libraries=thread,regex
>>>> ./bjam
>>>> ./bjam install --prefix=$HOME
>>>>
>>>> Then:
>>>> Code:
>>>>
>>>> cd mira-3.2.1
>>>> ./configure --with-boost=$HOME
>>>> make
>>>> make check
>>>>
>>>
>>>
>>> --
>>> Sebastian Jünemann
>>> CeBiTec - Center for Biotechnology
>>> Bielefeld University, D-33594 Bielefeld, Germany
>>> Office: V6-147 -- Phone: +49-(0)521-106-4827
>>> eMail: jueneman@xxxxxxxxxxxxxxxxxxxxxxxx
>>>
>>> --
>>> You have received this mail because you are subscribed to the mira_talk
>>> mailing list. For information on how to subscribe or unsubscribe,
>>>please
>>> visit http://www.chevreux.org/mira_mailinglists.html
>>
>>
>
>
>--
>Sebastian Jünemann
>CeBiTec - Center for Biotechnology
>Bielefeld University, D-33594 Bielefeld, Germany
>Office: V6-147 -- Phone: +49-(0)521-106-4827
>eMail: jueneman@xxxxxxxxxxxxxxxxxxxxxxxx
>
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