enable FreeType in local GB compile

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Hoover, David (NIH/CIT) [E]

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May 25, 2021, 4:26:35 PM5/25/21
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Hi all,

The latest versions of the Genome Browser now have a new feature, FreeType. We have the FreeType package locally installed, but yet I can't seem to have it enabled during the build. Is there some other trick to have it locate the FreeType libraries on the host?

David
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David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoov...@hpc.nih.gov

Brian Lee

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May 25, 2021, 4:43:27 PM5/25/21
to Hoover, David (NIH/CIT) [E], genome-mirror

Dear David,

Thanks for reaching out to the Genome Browser support team regarding freeType fonts. One of our engineers suggests the following solution:

Install FreeType and add the following line to your inc/common.mk file:

HG_INC+=-I/usr/include/freetype2 -DUSE_FREETYPE

Alternately, there is a way to turn off the font options via hg.conf with “freeType=off” as a setting.

Please note that we now distribute the fonts in the htdocs/urw-fonts directory, available here:

rsync rsync://hgdownload.soe.ucsc.edu/htdocs/urw-fonts/

I hope this works for your mirror! For further communication, please reply-all to genome...@soe.ucsc.edu. Those emails are archived in a public forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,


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Brian Lee

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May 25, 2021, 6:46:43 PM5/25/21
to Hoover, David (NIH/CIT) [E], genome-mirror

Dear David,

Thank you for sharing the experiences with FreeType errors when compiling.

We have updated our src/inc/common.mk file to have improved checks for freetype-config existence and you can get the lastest version here:
https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/inc/common.mk

Or see the specific changes here:
https://genome-source.gi.ucsc.edu/gitlist/kent.git/commit/8fff967390b185e152a6faf2a7335e5db23a9ff7

Thank you again for sharing these experiences and helping us improve the UCSC Genome Browser for mirror administrators!

All the best,

Michael Hiller

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Nov 2, 2022, 11:36:37 AM11/2/22
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Dear UCSC team,

I git pulled the latest code and now have a linking problem with ixIxx:

kent/src/index/ixIxx (master)$ cc -O -g -o /home/mhiller/bin/x86_64/ixIxx ixIxx.o ../../lib/x86_64/jkweb.a -L/usr/lib64/ -lmariadb -lstdc++ -lrt -lfreetype -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lm -lz -liconv -lm
../../lib/x86_64/jkweb.a(trix.o): In function `initCharTables':
/genome/src/kent/src/lib/trix.c:822: multiple definition of `initCharTables'
ixIxx.o:/genome/src/kent/src/index/ixIxx/ixIxx.c:51: first defined here
../../lib/x86_64/jkweb.a(trix.o): In function `skipToWord':
/genome/src/kent/src/lib/trix.c:836: multiple definition of `skipToWord'
ixIxx.o:/genome/src/kent/src/index/ixIxx/ixIxx.c:70: first defined here
../../lib/x86_64/jkweb.a(trix.o): In function `skipOutWord':
/genome/src/kent/src/lib/trix.c:850: multiple definition of `skipOutWord'
ixIxx.o:/genome/src/kent/src/index/ixIxx/ixIxx.c:84: first defined here
collect2: error: ld returned 1 exit status

The problem is that several functions that were originally only included in ixIxx.c are now also added to ../../lib/trix.c
which makes the linker complain.

grep initCharTables ../../* -R
../../hg/oneShot/testIndex/testIndex.c:void initCharTables()
../../hg/oneShot/testIndex/testIndex.c:initCharTables();
../../inc/trix.h:void initCharTables();
../../index/ixIxx/ixIxx.c:void initCharTables()
../../index/ixIxx/ixIxx.c:initCharTables();
Binary file ../../index/ixIxx/ixIxx.o matches
../../lib/trix.c:void initCharTables()
../../lib/trix.c:initCharTables();

git log shows that these functions were added 3 weeks ago with commit af3a143571.


Thanks a lot
- Michael

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