Re: GCC error and libmpfr.so.4 not found

Hi Jimmy,

I checked linkage with ldd:

ldd /path/to/cc1

Here is the result:

linux-vdso.so.1 => (0x00007fffed53f000)
libmpfr.so.4 =>
/../software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib/libmpfr.so.4
(0x00007f264f304000)
libgmp.so.10 =>
/../software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/lib/libgmp.so.10
(0x00007f264f08f000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000034a2800000)
libm.so.6 => /lib64/libm.so.6 (0x00000034a2000000)
libc.so.6 => /lib64/libc.so.6 (0x00000034a1c00000)
/lib64/ld-linux-x86-64.so.2 (0x00000034a1800000)

libmpfr.so.4 already exists but it still didn't find it.

I will now export LD_LIBRARY_PATH and see if it works..

Thank you,
Asma

On Thu, Jun 11, 2015 at 3:18 PM, Jimmy Yih <jyih(at)pivotal(dot)io> wrote:

> Hey Asma,
>
> Did you check the linkage with ldd? For example on my blank RHEL 6.5 AWS
> VM using gcc 4.4.7:
>
> [jyih(at)test1 ~]$ ldd /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/cc1
> linux-vdso.so.1 => (0x00007fff9b9ff000)
> libmpfr.so.1 => /usr/lib64/libmpfr.so.1 (0x00000033b8400000)
> libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00000033b8000000)
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003c1e400000)
> libc.so.6 => /lib64/libc.so.6 (0x0000003c1e800000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003c1e000000)
>
> Most likely you should have an empty/broken libmpfr.so linkage. You can
> play around with LD_LIBRARY_PATH like so:
> ## create another libmpfr.so link in a different directory for example
> [jyih(at)test1 ~]$ ls -al /usr/lib64/libmpfr*
> lrwxrwxrwx. 1 root root 16 Jun 7 2014 /usr/lib64/libmpfr.so.1 ->
> libmpfr.so.1.2.0
> -rwxr-xr-x. 1 root root 318408 Jun 23 2010 /usr/lib64/libmpfr.so.1.2.0
> [jyih(at)test1 ~]$ ln -s /usr/lib64/libmpfr.so.1.2.0 /tmp/libmpfr.so.1
>
> ## show that LD_LIBRARY_PATH is empty and then add new paths
> [jyih(at)test1 ~]$ echo $LD_LIBRARY_PATH
>
> [jyih(at)test1 ~]$ export LD_LIBRARY_PATH=/tmp:$LD_LIBRARY_PATH
>
> ## ldd shows new linking
> [jyih(at)test1 ~]$ ldd /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/cc1
> linux-vdso.so.1 => (0x00007fff06dff000)
> libmpfr.so.1 => /tmp/libmpfr.so.1 (0x00000033b8400000)
> libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00000033b8000000)
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003c1e400000)
> libc.so.6 => /lib64/libc.so.6 (0x0000003c1e800000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003c1e000000)
>
> Hope that helps!
>
> - Jimmy
>
> On Thu, Jun 11, 2015 at 11:44 AM, Asma Riyaz <asmariyaz23(at)gmail(dot)com>
> wrote:
>
>> Hi Jimmy,
>>
>> Here is what I did upon your suggestion;
>>
>> in bashrc:-
>>
>> LD_LIBRARY_PATH=/seq/annotation/bio_tools/BOOST/boost_1_46_1/lib
>>
>> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/seq/regev_genome_portal/lib
>>
>> sourced it and then exceuted /.configure as below:
>>
>> ./configure --prefix=/../../DATABASE/postgres
>>
>> I get the same error log as before.
>>
>> Asma
>>
>>
>>
>>
>>
>> On Thu, Jun 11, 2015 at 1:30 PM, Jimmy Yih <jyih(at)pivotal(dot)io> wrote:
>>
>>> Hey Asma,
>>>
>>> Have you tried running ldd and checking the library linkage? You might
>>> be able to just add the different location to your LD_LIBRARY_PATH as a
>>> quick way to get this working.
>>>
>>> - Jimmy
>>>
>>> On Thu, Jun 11, 2015 at 7:46 AM, Asma Riyaz <asmariyaz23(at)gmail(dot)com>
>>> wrote:
>>>
>>>> I have a libmpfr.so.4 under a different location, which setting in
>>>> configure should I use so that it uses the required library from that
>>>> directory?
>>>>
>>>> I have used ./configure --prefix=/path/directory
>>>> LIB=/path/to/libmpfr.so.4 but the config.log still shows that its looking
>>>> for libmpfr.so.4 under the shared location as before. Any advice will be
>>>> helpful.
>>>>
>>>> Thank you,
>>>> Asma
>>>>
>>>> On Thu, Jun 11, 2015 at 10:34 AM, Geoff Winkless <pgsqladmin(at)geoff(dot)dj>
>>>> wrote:
>>>>
>>>>> On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23(at)gmail(dot)com> wrote:
>>>>>
>>>>>> I have seen an earlier post with gcc errors, however I couldn't
>>>>>> figure out what the actual problem here is: is it that libmpfr.so.4 is not
>>>>>> found? or gcc needs to be installed fresh?
>>>>>>
>>>>>
>>>>> libmpfr. Unless I've misunderstood, the other errors are simply
>>>>> configure trying to work out which compiler you're running - -V and
>>>>> -qversion simply aren't valid flags to gcc - so those "error" lines are
>>>>> expected result.
>>>>>
>>>>> Geoff
>>>>>
>>>>>
>>>>
>>>
>>
>