curl error during make: install failure about glactools HOT 6 CLOSED

just so I can diagnose a bit better, could you go in the glactools directory, then do:

cd htslib
make clean
make

from glactools.

Here is what I got:

glactools$ cd htslib
htslib$ make clean
rm -f test/.tmp test/.tmp.* test/tabix/.tmp. test/tabix/FAIL*
rm -f .o .pico cram/.o cram/.pico test/.o test/.dSYM version.h
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/sam test/test_bgzf test/test_kstring test/test_realn test/test-regidx test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7
htslib$ make
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -c -o header.o header.c
gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-288-g830c061"' > version.h
gcc -g -Wall -O2 -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I. -c -o realn.o realn.c
gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I. -c -o region.o region.c
gcc -g -Wall -O2 -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -I. -fpic -c -o header.pico header.c
gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -I. -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -I. -fpic -c -o region.pico region.c
gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -Wall -O2 -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-soname,libhts.so.2to3part10 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
ln -sf libhts.so libhts.so.2to3part10
gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c
gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c
gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c
gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma -lcurl
gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c
gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/pileup.o test/pileup.c
gcc -o test/pileup test/pileup.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c
gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_realn.o test/test_realn.c
gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c
gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_index.o test/test_index.c
gcc -o test/test_index test/test_index.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
htslib$

from glactools.

so htslib has built successfully?

from glactools.

Well, no errors were produced... So I guess that means Yes

from glactools.

it seems to have worked, from there, can you do a
cd ..
and

make
and post the output?

from glactools.

You wrote email to say you updated the makefile. I re-cloned the repo and then compiled. It finished without errors :-) I will test this as soon as I get the chance. Thanks for addressing this issue.
Cheers,
Peter

from glactools.