[EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GDerror)?
Chenggang Zhang
zhangcg at bmi.ac.cn
Mon Jul 30 12:07:15 UTC 2007
Dear Dr. Aln,
Thank you for the kind suggestion. The installation is now OK using the following command:
'./configure --with-pngdriver=/usr/local'
Best regards,
Sincerely yours,
Chenggang Zhang
2007-07-30 20:06:16
==============================================
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 yahoo.com, zcgweb at gmail.com
==============================================
=======Your original message at 2007-07-30 16:23:07=======
>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
>>
>> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
>> support
>> Next message: [EMBOSS] Sixpack
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> --------------------------------------------------------------------------------
>>
>> 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/
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
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>>
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