Thanks a lot to you all, A combination of Carlos and UCSC gave me a go. my final .bashrc now contains ...
# for UCSC & Jim Kent src export MACHTYPE=i386 # use png from X11 which seems to be better accepted tan the mac port version export PNGINCL=-I/usr/X11/include/libpng12 export PNGLIB=/usr/X11/lib/libpng12.dylib # MYSQL not really used as I do not mirror the UCSC HG export MYSQLLIBS="/usr/local/mysql/lib/libmysqlclient.a -lmysqlclient -lpthread" export MYSQLINC="/usr/local/mysql/include" # my bam is elsewhere, installed with mac port export USE_BAM=1 export SAMINC=/opt/local/include/bam export SAMDIR=/opt/local/lib Thanks again, I hope this will help others Stephane On 02 Apr 2011, at 03:49, Carlos Javier Borroto wrote: > This is what I have in my ~/.bash_profile in Mac OS X 10.6.7: > # Genome Browser > export MYSQLINC=/usr/local/include > export MYSQLLIBS="-L/usr/local/Cellar/mysql/5.5.10/lib -lmysqlclient > -lpthread -lz -lssl -lcrypto" > export MACHTYPE=x86_64 > export PNGINCL=-I/usr/X11/include/libpng12 > export PNGLIB=/usr/X11/lib/libpng12.dylib > export USE_BAM=1 > export SAMINC=/usr/local/include/bam > export SAMDIR=/usr/local/lib > > This use libpng that comes with Mac OS X I see you seems to be using > something out of /opt, maybe you could give it a try to use the system > libs. And regarding MySQL and Samtools installation to match the rest > of these exports, I use Homebrew(http://mxcl.github.com/homebrew/). > > Hope it helps > -- > Carlos Borroto > Baltimore, MD > > > > 2011/4/1 Stéphane Plaisance <[email protected]>: >> Dear >> >> I have a problem related to one posted @ >> http://www.mail-archive.com/[email protected]/msg02853.html >> >> my machine is OSX 10.6.7 >> I build in ~/bin/kent/src >> I have MACHTYPE set to i386 >> I have ~/bin/i386 in my PATH >> >> I just downloaded the latest source jksrc.zip and at make stage it dies with: >> >> gcc -O -g -Wall -Wno-unused-variable -D_FILE_OFFSET_BITS=64 >> -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i386 -DUSE_SSL -DCOLOR32 >> -Wall -Wno-unused-variable -I../inc -I../../inc -I../../../inc >> -I../../../../inc -I../../../../../inc -o pngwrite.o -c pngwrite.c >> pngwrite.c:7:87: error: png.h: No such file or directory >> pngwrite.c:13: error: expected ')' before 'png' >> pngwrite.c:19: error: expected ')' before 'png' >> pngwrite.c: In function 'mgSaveToPng': >> pngwrite.c:34: error: 'png_structp' undeclared (first use in this function) >> pngwrite.c:34: error: (Each undeclared identifier is reported only once >> pngwrite.c:34: error: for each function it appears in.) >> pngwrite.c:34: error: expected ';' before 'png' >> pngwrite.c:37: error: 'png' undeclared (first use in this function) >> pngwrite.c:42: error: 'png_infop' undeclared (first use in this function) >> pngwrite.c:42: error: expected ';' before 'info' >> pngwrite.c:43: error: 'info' undeclared (first use in this function) >> pngwrite.c:46: warning: implicit declaration of function >> 'png_destroy_write_struct' >> pngwrite.c:52: warning: implicit declaration of function 'png_jmpbuf' >> pngwrite.c:52: warning: passing argument 1 of 'setjmp' makes pointer from >> integer without a cast >> pngwrite.c:62: warning: implicit declaration of function 'png_init_io' >> pngwrite.c:64: warning: implicit declaration of function 'png_set_IHDR' >> pngwrite.c:65: error: 'PNG_COLOR_TYPE_RGBA' undeclared (first use in this >> function) >> pngwrite.c:65: error: 'PNG_INTERLACE_NONE' undeclared (first use in this >> function) >> pngwrite.c:66: error: 'PNG_COMPRESSION_TYPE_DEFAULT' undeclared (first use >> in this function) >> pngwrite.c:66: error: 'PNG_FILTER_TYPE_DEFAULT' undeclared (first use in >> this function) >> pngwrite.c:91: error: 'png_byte' undeclared (first use in this function) >> pngwrite.c:91: error: 'row_pointers' undeclared (first use in this function) >> pngwrite.c:91: error: expected expression before ')' token >> pngwrite.c:95: warning: implicit declaration of function 'png_set_rows' >> pngwrite.c:96: warning: implicit declaration of function 'png_write_png' >> pngwrite.c:96: error: 'PNG_TRANSFORM_IDENTITY' undeclared (first use in this >> function) >> make[1]: *** [pngwrite.o] Error 1 >> make: *** [topLibs] Error 2 >> >> I did a make clean and tried again >> >> nope >> >> I exported PNGLIB by two ways with success declaring but failure building >> >> * export PNGLIB=/opt/local/lib/libpng.a >> $ echo $PNGLIB >> /opt/local/lib/libpng.a >> >> * export PNGLIB='-L/opt/local/lib -lpng' >> $ echo $PNGLIB >> -L/opt/local/lib -lpng >> >> I made sure libpng was installed using mac port >> >> $locate libpng.a >> /opt/local/lib/libpng.a >> /opt/local/var/macports/software/libpng/1.2.44_0/opt/local/lib/libpng.a >> /opt/local/var/macports/software/libpng/1.4.5_0/opt/local/lib/libpng.a >> >> $ ll /opt/local/lib/libpng* >> lrwxr-xr-x 1 root admin 10 Mar 8 18:26 libpng.a -> libpng14.a >> lrwxr-xr-x 1 root admin 14 Mar 8 18:26 libpng.dylib -> libpng14.dylib >> lrwxr-xr-x 1 root admin 11 Mar 8 18:26 libpng.la -> libpng14.la >> -rwxr-xr-x 2 root admin 160K Mar 8 18:26 libpng14.14.dylib >> -rw-r--r-- 2 root admin 220K Mar 8 18:26 libpng14.a >> lrwxr-xr-x 1 root admin 17 Mar 8 18:26 libpng14.dylib -> >> libpng14.14.dylib >> -rwxr-xr-x 2 root admin 941 Mar 8 18:26 libpng14.la >> >> (libpng @1.4.5_0 (active)) >> >> What can I do to fix this lib issue please? >> >> Thanks in advance, >> Stephane >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
