[EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GD error)?
ajb at ebi.ac.uk
ajb at ebi.ac.uk
Mon Jul 30 08:22:53 UTC 2007
Dear Chenggang Zhang,
There is insufficient detail in your message to be able to answer
it definitively, except to say that it is a GD error. In general:
1) If the GD update is from RPMs that put the gd and gd-devel
files in the standard RH9 system area (unlikely I suppose as
RH9 is so old) then you should just do a 'make clean' and
'./configure' EMBOSS again.
2) If you've compiled gd yourself and the libraries are
in (e.g.) /usr/local/lib and the headers under /usr/local/include
then, again, 'make clean' but this time add the
--with-pngdriver=/usr/local
switch to the './configure' line. (Amend /usr/local appropriately
if you put the gd files elsewhere).
HTH
Alan
> Dear EMBOSS maintainer,
>
> I have the similary question as Christian reported below. However, even if
> I have updated the GD to version 2.0.28 or 2.0.35, I still failed to
> install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp
> #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver
> 9.0). The error information was attached below. Could you please tell me
> how to solve this question?
>
> make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss'
> /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o aaindexextract
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la
> ../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11 -lm
> -lgd
> -lpng -lz -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib
> -lX11 -lgd -lpng -lz -lm -Wl,--rpath -Wl,/usr/local/emboss5/lib
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetThickness'
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageCreateTrueColor'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetAntiAliased'
> collect2: ld returned 1 exit status
> make[2]: *** [aaindexextract] Error 1
> make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make: *** [all-recursive] Error 1
>
> Best regards,
>
> Sincerely yours,
> Chenggang Zhang
> 2007.07.30 15:36:41
>
> ==============================================
> Chenggang Zhang, PhD, Professor and Director
> Department of Neurobiology
> Beijing Institute of Radiation Medicine
> Taiping Road 27, Beijing, 100850, China.
> Tel: +8610-66931590. Fax: +8610-68169574
> Cell phone: +8610-13910133213
> Email: zhangcg at bmi.ac.cn, zcgweb at 126.com
> zcgweb at gmail.com, zcgweb at yahoo.com
> ==============================================
>
>
>>================================================================================================================
> [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
> ajb at ebi.ac.uk ajb at ebi.ac.uk
> Mon Jul 16 12:23:47 EDT 2007
>
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> --------------------------------------------------------------------------------
>
> Dear Christian,
>
> Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
> mentioned in the announcement, just install an up-to-date gd2 on SLES 9
> and the compilation will work.
>
> I've updated the development version of README to reflect this.
>
> Alan
>
>
>
>> Dear EMBOSS maintainer
>>
>> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
>> fails, while linking:
>>
>> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so
>> -L/usr/X11R6/lib64
>> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
>> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
>> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>>
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>>
>> Configuration:
>> ./configure --prefix=/usr/local/emboss5
>>
>> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
>> the fact that newer Versions of
>> gd don't support gif anymore (cf. README line 65).
>>
>> Is there any workarround for the problem (I don't bother changing code)?
>>
>> Best regards
>> Christian
>> --
>> =============================================================================
>> Christian Bolliger
>> IT Services | http://www.id.uzh.ch/
>> Central Systems / HPC | http://www.matterhorn.uzh.ch/
>> University of Zuerich | E-Mail: christian.bolliger at
>> id.uzh.ch
>> Winterthurerstr. 190 | Tel: +41 (0)1 63 56775
>> CH-8057 Zuerich; Switzerland | Fax: +41 (0)1 63 54505
>> Mime/S CA: https://www.ca.unizh.ch/client/
>>
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>>
>
>
>
>
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