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 <j...@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 <asmariya...@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 <j...@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 <asmariya...@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 <pgsqlad...@geoff.dj> >>>> wrote: >>>> >>>>> On 11 June 2015 at 15:20, Asma Riyaz <asmariya...@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 >>>>> >>>>> >>>> >>> >> >
