gpertea
commented
4 years ago fatal error: zlib.h: No such file or directory
It looks like the zlib development package is not installed on your system. Depending on your Linux distribution the package to be installed can have different names (zlib-devel for RedHat based systems, zlib1g-dev for Debian based systems etc.)
Dear gpertea, The program installation failed course of './samtools-0.1.18/bgzf.h:29:10: fatal error: zlib.h: No such file or directory'
The following is all report during installing: make release cd ./samtools-0.1.18 && make lib make[1]: Entering directory '/home/tanghongzhen/software/stringtie-2.1.3/samtools-0.1.18' gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o bgzf.c: In function ‘bgzf_check_EOF’: bgzf.c:677:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^
~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_load_core’: bam_index.c:330:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~ bam_index.c:337:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~ bam_index.c:350:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~~ bam_index.c:353:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~bam_index.c:357:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~~ bam_index.c:361:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~~~~ bam_index.c:371:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~~~ bam_index.c:375:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o razf.c: In function ‘razf_flush’: razf.c:223:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~ razf.c:236:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~ razf.c: In function ‘_razf_write’: razf.c:203:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_open_r’: razf.c:422:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd, &end, sizeof(int64_t)); ^~~~~~~razf.c:430:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd, &end, sizeof(int64_t)); ^~~~~~~razf.c: In function ‘load_zindex’: razf.c:124:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~ razf.c:133:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd, rz->index->bin_offsets, sizeof(int64_t) v32); ^~~~~~~~~~~~~~~ razf.c:139:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd, rz->index->cell_offsets, sizeof(int) rz->index->size); ^~~~~~~~~~~~~~~~ razf.c: In function ‘razf_close’: razf.c:815:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, &rz->in, sizeof(int64_t)); ^~~~~~~~~~~~ razf.c:816:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~~~ razf.c:819:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, &v64, sizeof(int64_t)); ^~~~~~~~~razf.c:821:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, &v64, sizeof(int64_t)); ^~~~~~~~~razf.c: In function ‘razf_end_flush’: razf.c:260:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~ razf.c: In function ‘save_zindex’: razf.c:96:12: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~ razf.c:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~ razf.c:106:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) v32); ^~~~~~~~~~~~razf.c:107:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) rz->index->size); ^~~~~~~~~~~~~~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o In file included from bam_sort.c:9:0: bam_sort.c:309:26: warning: ‘bam1_lt’ is static but used in inline function ‘ks_insertsort_sort’ which is not static KSORT_INIT(sort, bam1_p, bam1_lt) ^ ksort.h:148:25: note: in definition of macro ‘KSORT_INIT’ for (j = i; j > s && sort_lt(j, (j-1)); --j) { \ ^~~~~ bam_sort.c:53:27: warning: ‘heap_lt’ is static but used in inline function ‘ks_insertsort_heap’ which is not static KSORT_INIT(heap, heap1_t, heap_lt) ^ ksort.h:148:25: note: in definition of macro ‘KSORT_INIT’ for (j = i; j > s && sort_lt(j, (j-1)); --j) { \ ^~~~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:11:16: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] bam_header_t *old; ^~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^~~ gcc -c -g -Wall -fsigned-char -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o /home/tanghongzhen/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[1]: Leaving directory '/home/tanghongzhen/software/stringtie-2.1.3/samtools-0.1.18' /home/tanghongzhen/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -pthread -c gclib/GBase.cpp -o gclib/GBase.o /home/tanghongzhen/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o /home/tanghongzhen/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -pthread -c gclib/GStr.cpp -o gclib/GStr.o /home/tanghongzhen/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -pthread -c gclib/GBam.cpp -o gclib/GBam.o In file included from ./samtools-0.1.18/bam.h:52:0, from gclib/GBam.h:5, from gclib/GBam.cpp:1: ./samtools-0.1.18/bgzf.h:29:10: fatal error: zlib.h: No such file or directoryinclude
compilation terminated. make: *** [Makefile:139: gclib/GBam.o] Error 1