enable FreeType in local GB compile

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Hoover, David (NIH/CIT) [E]

May 25, 2021, 4:26:35 PM5/25/21
to genome-mirror
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 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

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

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:

Or see the specific changes here:

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

All the best,

Michael Hiller

Nov 2, 2022, 11:36:37 AM11/2/22
to genome-mirror
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()
../../inc/trix.h:void initCharTables();
../../index/ixIxx/ixIxx.c:void initCharTables()
Binary file ../../index/ixIxx/ixIxx.o matches
../../lib/trix.c:void initCharTables()

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

Thanks a lot
- Michael

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