GCC error and libmpfr.so.4 not found

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

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@geoff.dj>
wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

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@gmail.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@geoff.dj>
wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

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@pivotal.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@gmail.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@geoff.dj>
wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

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@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@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@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@test1 ~]$ echo $LD_LIBRARY_PATH

[jyih@test1 ~]$ export LD_LIBRARY_PATH=/tmp:$LD_LIBRARY_PATH

## ldd shows new linking
[jyih@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@gmail.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@pivotal.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@gmail.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@geoff.dj>
wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

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@pivotal.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@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@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@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@test1 ~]$ echo $LD_LIBRARY_PATH

[jyih@test1 ~]$ export LD_LIBRARY_PATH=/tmp:$LD_LIBRARY_PATH

## ldd shows new linking
[jyih@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@gmail.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@pivotal.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@gmail.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@geoff.dj>
wrote:

On 11 June 2015 at 15:20, Asma Riyaz <asmariyaz23@gmail.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

regards, tom lane

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