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Old 10-26-2010, 02:15 PM   #1
feng
Member
 
Location: US

Join Date: Oct 2010
Posts: 50
Default any help for this compile problem with SRA_SDK?

I got this trouble with compiling SRA_sdk-1.0.0-b10 with a Mac. Any help for this problem? Thanks for any hit.


shyadminpcp1454:/ feng$ OUTDIR=/

shyadminpcp1454:sra_sdk-1.0.0-b10 feng$ make OUTDIR="$OUTDIR" out

shyadminpcp1454:sra_sdk-1.0.0-b10 feng$ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OUTDIR/lib64:$OUTDIR/ilib64"

shyadminpcp1454:sra_sdk-1.0.0-b10 feng$ make

gcc -c -o text.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/text.c
ar -rc //rel/gcc/x86_64/ilib/libktxt.a text.pic.o
gcc -c -o text.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/text.c
ar -rc //rel/gcc/x86_64/ilib/libktxt.log.a text.log.pic.o
gcc -c -o utf8.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/utf8.c
ar -rc //rel/gcc/x86_64/ilib/libkutf8.a utf8.pic.o
gcc -c -o utf8.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/utf8.c
ar -rc //rel/gcc/x86_64/ilib/libkutf8.log.a utf8.log.pic.o
gcc -c -o iso8859.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/iso8859.c
gcc -c -o iso8859-1.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/iso8859-1.c
gcc -c -o cp1252.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/cp1252.c
ar -rc //rel/gcc/x86_64/ilib/libkiso8859.a iso8859.pic.o iso8859-1.pic.o cp1252.pic.o
gcc -c -o iso8859.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/iso8859.c
gcc -c -o iso8859-1.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/iso8859-1.c
gcc -c -o cp1252.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/cp1252.c
ar -rc //rel/gcc/x86_64/ilib/libkiso8859.log.a iso8859.log.pic.o iso8859-1.log.pic.o cp1252.log.pic.o
gcc -c -o token.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/token.c
gcc -c -o symtab.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/symtab.c
ar -rc //rel/gcc/x86_64/ilib/libktok.a token.pic.o symtab.pic.o
gcc -c -o token.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/token.c
gcc -c -o symtab.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/symtab.c
ar -rc //rel/gcc/x86_64/ilib/libktok.log.a token.log.pic.o symtab.log.pic.o
gcc -c -o ascii.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix/ascii.c
ar -rc //rel/gcc/x86_64/lib/libkascii.1.0.1.a ascii.pic.o
ln -s libkascii.1.0.1.a //rel/gcc/x86_64/lib/libkascii.a
gcc -dynamiclib -o //rel/gcc/x86_64/lib/libkascii.1.0.1.dylib -compatibility_version 1 -current_version 1.0.1 -flat_namespace -undefined suppress -O3 -arch x86_64 ascii.pic.o
ln -s libkascii.1.0.1.dylib //rel/gcc/x86_64/lib/libkascii.1.dylib
ln -s libkascii.1.dylib //rel/gcc/x86_64/lib/libkascii.dylib
gcc -c -o ascii.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/txt/unix/ascii.c
ar -rc //rel/gcc/x86_64/ilib/libkascii.log.a ascii.log.pic.o
gcc -c -o systimeout.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:27:23: error: os-native.h: No such file or directory
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:42: error: syntax error before ‘*’ token
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c: In function ‘TimeoutInit’:
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:44: error: ‘tm’ undeclared (first use in this function)
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:44: error: (Each undeclared identifier is reported only once
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:44: error: for each function it appears in.)
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:47: error: ‘msec’ undeclared (first use in this function)
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c: At top level:
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:56: error: syntax error before ‘*’ token
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c: In function ‘TimeoutPrepare’:
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:58: error: ‘self’ undeclared (first use in this function)
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:63: error: storage size of ‘tv’ isn’t known
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:64: error: storage size of ‘tz’ isn’t known
/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c:78: error: ‘time_t’ undeclared (first use in this function)
make[3]: *** [systimeout.pic.o] Error 1
make[2]: *** [std] Error 2
make[1]: *** [proc] Error 2
make: *** [klib] Error 2
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Old 10-26-2010, 08:54 PM   #2
dawe
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I guess you have to substitute any

Code:
#include <time.h>
with

Code:
#include <sys/time.h>
in the source tree. BTW I don't have that SDK, can you provide a link to download?

d
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Old 10-27-2010, 05:20 AM   #3
feng
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http://www.ncbi.nlm.nih.gov/Traces/s...are&s=software

from above link, can you try it? How is your installation?
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Old 10-27-2010, 05:30 AM   #4
feng
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Can you tell me a little more on 'time.h'? Which file should I look for it? Thanks.
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Old 10-27-2010, 06:53 AM   #5
dawe
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Quote:
Originally Posted by feng View Post
http://www.ncbi.nlm.nih.gov/Traces/s...are&s=software

from above link, can you try it? How is your installation?
OMG, this is one excellent example of bad portability :-(
Code is full of function that are not part of BSD libc... I've found a solution implementing what's linked here. In the end you should be able to build on Snow Leopard applying this patch

Code:
diff -Naur sra_sdk-1.0.0-b10/inc/mac/misstring.h sra_sdk-1.0.0-b10_sl/inc/mac/misstring.h
--- sra_sdk-1.0.0-b10/inc/mac/misstring.h       1970-01-01 01:00:00.000000000 +0100
+++ sra_sdk-1.0.0-b10_sl/inc/mac/misstring.h    2010-10-27 16:51:26.000000000 +0200
@@ -0,0 +1,2 @@
+char *strndup (char const *s, size_t n);
+size_t strnlen (const char *string, size_t maxlen);
diff -Naur sra_sdk-1.0.0-b10/inc/mac/os-native.h sra_sdk-1.0.0-b10_sl/inc/mac/os-native.h
--- sra_sdk-1.0.0-b10/inc/mac/os-native.h	1970-01-01 01:00:00.000000000 +0100
+++ sra_sdk-1.0.0-b10_sl/inc/mac/os-native.h	2010-10-27 15:36:01.000000000 +0200
@@ -0,0 +1,34 @@
+/*===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+*/
+
+#ifndef _h_os_native_
+#define _h_os_native_
+
+#ifndef _h_unix_native_
+#include "../unix/unix-native.h"
+#endif
+
+#endif /* _h_os_native_ */
diff -Naur sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c sra_sdk-1.0.0-b10_sl/klib/proc/unix/systimeout.c
--- sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c	2009-10-02 18:57:35.000000000 +0200
+++ sra_sdk-1.0.0-b10_sl/klib/proc/unix/systimeout.c	2010-10-27 15:30:31.000000000 +0200
@@ -28,7 +28,6 @@
 #include <kapp/log.h>
 #include <klib/rc.h>
 
-
 /*--------------------------------------------------------------------------
  * timeout_t
  *  a structure for communicating a timeout
diff -Naur sra_sdk-1.0.0-b10/klib/xml/xml.c sra_sdk-1.0.0-b10_sl/klib/xml/xml.c
--- sra_sdk-1.0.0-b10/klib/xml/xml.c	2010-05-19 22:11:33.000000000 +0200
+++ sra_sdk-1.0.0-b10_sl/klib/xml/xml.c	2010-10-27 16:02:19.000000000 +0200
@@ -38,10 +38,32 @@
 #include <libxml/xpath.h>  /* xmlXPathContextPtr */
 
 #include <assert.h>        /* assert */
+#include <sys/conf.h>
 #include <string.h>        /* strdup */
 #include <os-native.h>     /* strndup */
+#include <misstring.h>
 #include <strtol.h>        /* strtoXX */
 
+
+size_t
+strnlen (const char *string, size_t maxlen)
+{
+  const char *end = memchr (string, '\0', maxlen);
+  return end ? (size_t) (end - string) : maxlen;
+}
+
+char *
+strndup (char const *s, size_t n)
+{
+  size_t len = strnlen (s, n);
+  char *new = malloc (len + 1);
+
+  if (new == NULL)
+    return NULL;
+
+  new[len] = '\0';
+  return memcpy (new, s, len);
+}
 /********* XML manager ********/
 
 struct KXMLMgr {
diff -Naur sra_sdk-1.0.0-b10/sra/tools/dumper-fastq.c sra_sdk-1.0.0-b10_sl/sra/tools/dumper-fastq.c
--- sra_sdk-1.0.0-b10/sra/tools/dumper-fastq.c	2010-05-20 17:07:44.000000000 +0200
+++ sra_sdk-1.0.0-b10_sl/sra/tools/dumper-fastq.c	2010-10-27 16:02:29.000000000 +0200
@@ -54,6 +54,8 @@
 Corresponding reads in the paired files will occur at the same line in each file.
 
 */
+
+#include <sys/conf.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -68,6 +70,28 @@
 #include "dumper-core.h"
 #include "fastq-dump2.vers.h"
 
+#include <misstring.h>
+
+size_t
+strnlen (const char *string, size_t maxlen)
+{
+  const char *end = memchr (string, '\0', maxlen);
+  return end ? (size_t) (end - string) : maxlen;
+}
+
+
+char *
+strndup (char const *s, size_t n)
+{
+  size_t len = strnlen (s, n);
+  char *new = malloc (len + 1);
+
+  if (new == NULL)
+    return NULL;
+
+  new[len] = '\0';
+  return memcpy (new, s, len);
+}
 struct FastqArgs_struct {
     uint8_t platform;
just copy it into a file and then

Code:
$ cd sra_sdk-1.0.0-b10
$ patch -p1 < path/to/the/patch/above
$ make
It should work

Code:
$ uname -a
Darwin host036.2b11.ifom-ieo-campus.it 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386
$ gcc -v
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc/gcc-5664~105/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5664)
HTH

d
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Old 10-27-2010, 07:56 AM   #6
feng
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Join Date: Oct 2010
Posts: 50
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Hi Dawe, Thank so much for this help. I got another error. This may come from 'Leopard'?? I really need your great help again with many thanks.

$ uname -a
Darwin shyadminpcp1454.remotes.upmc.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

$ gcc -v
Using built-in specs.
Target: i686-apple-darwin9
Configured with: /var/tmp/gcc/gcc-5490~1/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9
Thread model: posix
gcc version 4.0.1 (Apple Inc. build 5490)

$ make
make[3]: Nothing to be done for `//rel/gcc/x86_64/std'.
gcc -c -o systimeout.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/proc/unix/systimeout.c

........


gcc -c -o sysmain.pic.o -fPIC -O3 -arch x86_64 -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/unix/sysmain.c
ar -rc //rel/gcc/x86_64/ilib/libkapp.a main.pic.o sysmain.pic.o
gcc -c -o main.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/main.c
gcc -c -o sysmain.log.pic.o -fPIC -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/app/unix/sysmain.c
ar -rc //rel/gcc/x86_64/ilib/libkapp.log.a main.log.pic.o sysmain.log.pic.o
gcc -c -o rcexplain.o -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/rcexplain.c
gcc -o //rel/gcc/x86_64/bin/rcexplain.1.0.2 -O3 -arch x86_64 rcexplain.o -L//rel/gcc/x86_64/lib -lktlog -L//rel/gcc/x86_64/ilib -lkapp.log -lkascii.log -lktxt.log
ln -s rcexplain.1.0.2 //rel/gcc/x86_64/bin/rcexplain
gcc -c -o kdbmeta.o -O3 -arch x86_64 -D_LOGGING -DNDEBUG -DMAC -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/unix -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/itf -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc/x86_64 -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/gcc -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/mac -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/bsd -I/Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/inc/unix -MD /Users/feng/Documents/Lab_Data/DATA/454_sequencing/Data_Analysis/SRA/sra_sdk-1.0.0-b10/klib/tools/kdbmeta.c
gcc -o //rel/gcc/x86_64/bin/kdbmeta.1.0.0 -O3 -arch x86_64 kdbmeta.o -L//rel/gcc/x86_64/lib -lktlog -L//rel/gcc/x86_64/ilib -lkapp.log -lkdb.log -lkarc.log -lktar.log -lkfs.log -lkpt.log -lktrie.log -lkcont.log -lkascii.log -lktxt.log -lkpack.log -lkcs.log
ld warning: in //rel/gcc/x86_64/ilib/libkpt.log.a, file is not of required architecture
Undefined symbols:
"_PBSTreeForEach", referenced from:
_KTocInflatePBSTree in libkarc.log.a(tocentry.log.pic.o)
_ktocentryInflate in libkarc.log.a(tocentry.log.pic.o)
"_PBSTreeWhack", referenced from:
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KDBManagerOpenMetadataReadInt in libkdb.log.a(meta.log.pic.o)
"_BSTreePersist", referenced from:
_KTocEntryPersistNodeDir in libkarc.log.a(tocentry.log.pic.o)
_KTocEntryPersist in libkarc.log.a(tocentry.log.pic.o)
"_PBSTreeMake", referenced from:
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KDBManagerOpenMetadataReadInt in libkdb.log.a(meta.log.pic.o)
_KTocInflatePBSTree in libkarc.log.a(tocentry.log.pic.o)
_ktocentryInflate in libkarc.log.a(tocentry.log.pic.o)
"_PBSTreeDoUntil", referenced from:
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KDBManagerOpenMetadataReadInt in libkdb.log.a(meta.log.pic.o)
_KDBManagerOpenMetadataReadInt in libkdb.log.a(meta.log.pic.o)
"_PBSTreeSize", referenced from:
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
_KMDataNodeInflate in libkdb.log.a(meta.log.pic.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [//rel/gcc/x86_64/bin/kdbmeta] Error 1
make[2]: *** [std] Error 2
make[1]: *** [tools] Error 2
make: *** [klib] Error 2
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Old 10-28-2010, 12:10 AM   #7
dawe
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Quote:
Originally Posted by feng View Post
Hi Dawe, Thank so much for this help. I got another error. This may come from 'Leopard'?? I really need your great help again with many thanks.



ld warning: in //rel/gcc/x86_64/ilib/libkpt.log.a, file is not of required architecture
It is an error coming from OS X 10.5 (as you could read from the warnings). gcc default build architecture is i386 for OS X 10.5 and OS X 10.4. The makefiles don't set properly the correct CFLAGS so all you have to do is:
1- Inform the sra-sdk dev team about this bug
2- modify the build/Makefile.mac.gcc like this:

Code:
diff -u build/Makefile.mac.gcc*
--- build/Makefile.mac.gcc	2010-10-28 10:06:32.000000000 +0200
+++ build/Makefile.mac.gcc.x86_64	2010-10-28 10:06:13.000000000 +0200
@@ -24,8 +24,8 @@
 
 
 # compilers
-CC = gcc -c
-CP = g++ -c
+CC = gcc -c -arch x86_64
+CP = g++ -c -arch x86_64
 
 # linkers
 LD = $(TOP)/build/ld.mac.gcc.sh gcc
forcing the 64 bit architecture (unless you want the 32 bit one).
d
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