Error in Compilation cgpBigWig

[mattoslmp]

Dear Davir,
When I run the compilation (cgpBigWig) everything runs, but in the end I get an error bellow, any suggestion:

gcc -O3 -DVERSION='"0.4.4"' -g -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -Wall ./bam2bwbases.c ./bam_access.o ./utils.o -L./htslib_tmp -L/usr/local/ICGC/lib -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -lhts -lpthread -lz -lm -ldl -o ../bin/bam2bwbases
gcc -O3 -DVERSION='"0.4.4"' -g -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -Wall ./bwjoin.c ./bam_access.o ./utils.o -L./htslib_tmp -L/usr/local/ICGC/lib -lhts -lpthread -lz -lm -ldl -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o ../bin/bwjoin
gcc -O3 -DVERSION='"0.4.4"' -g -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -Wall ./catbw.c ./bam_access.o ./utils.o -L./htslib_tmp -L/usr/local/ICGC/lib -lhts -lpthread -lz -lm -ldl -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o ../bin/bwcat
gcc -O3 -DVERSION='"0.4.4"' -g -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -Wall ./bg2bw.c ./bam_access.o ./utils.o -L./htslib_tmp -L/usr/local/ICGC/lib -lhts -lpthread -lz -lm -ldl -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o ../bin/bg2bw
gcc -O3 -DVERSION='"0.4.4"' -g -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -Wall ./detectExtremeDepth.c ./bam_access.o ./utils.o -L./htslib_tmp -L/usr/local/ICGC/lib -lhts -lpthread -lz -lm -ldl -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o ../bin/detectExtremeDepth
remove tmp hts location
rm -rf ./htslib_tmp
gcc -O3 -DVERSION='"0.4.4"' -g -Wall -I/usr/local/ICGC/include -I/usr/local/cgpBigWig-0.4.4/install_tmp/htslib/ -rdynamic -I./ ./bam_access.o ./utils.o -L./htslib_tmp -lhts -lpthread -lz -lm -ldl -L/usr/local/ICGC/lib c_tests/utils_tests.c -o c_tests/utils_tests
./bam_access.o: In function process_bam_region_bases': /usr/local/cgpBigWig-0.4.4/c/bam_access.c:316: undefined reference to sam_index_load'
/usr/local/cgpBigWig-0.4.4/c/bam_access.c:334: undefined reference to sam_itr_querys' ./bam_access.o: In function process_bam_region':
/usr/local/cgpBigWig-0.4.4/c/bam_access.c:415: undefined reference to sam_index_load' /usr/local/cgpBigWig-0.4.4/c/bam_access.c:417: undefined reference to sam_itr_querys'
collect2: error: ld returned 1 exit status
make: *** [c_tests/utils_tests] Error 1
make: Leaving directory `/usr/local/cgpBigWig-0.4.4/c

Thanks,
Leandro

[ghost]

@mattoslmp Looks like cbpBigWig isn't seeing the sam.h include file. How have you installed this? Using the standard ./setup.sh /path/to/install?