Hi everyone... I think libmpfr.so.4 is being searched for in the /../software/free/Linux/ redhat_6_x86_64/pkgs/gcc_4.9.0/libexec (according to error message) directory but on our system it is located in /../software/free/Linux/ redhat_6_x86_64/pkgs/gcc_4.9.0/lib
Any idea how I can specify as to which directory should configure refer to for library directory? -Thank you, Asma On Thu, Jun 11, 2015 at 3:32 PM, Asma Riyaz <asmariya...@gmail.com> wrote: > 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 >>>>>> >>>>>> >>>>> >>>> >>> >> >
