Bio-DB-HTS failing install log

## Install Log

>> git clone https://github.com/Ensembl/Bio-DB-HTS.git
Cloning into 'Bio-DB-HTS'...
remote: Enumerating objects: 45, done.
remote: Counting objects: 100% (45/45), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 3693 (delta 17), reused 33 (delta 12), pack-reused 3648
Receiving objects: 100% (3693/3693), 9.98 MiB | 6.06 MiB/s, done.
Resolving deltas: 100% (1990/1990), done.
Checking connectivity... done.

(0)[16:33][pcarlton@chromosome-linux:~/code/vagrent]
>> cd Bio-DB-HTS/

(0)[16:33][pcarlton@chromosome-linux:~/code/vagrent/Bio-DB-HTS]
>> lr
total 368K
-rw-r--r-- 1 pcarlton 5.5K 2019-03-06 16:33:37.662169800 +0900 Build.PL
-rw-r--r-- 1 pcarlton 4.4K 2019-03-06 16:33:37.666169757 +0900 README
-rw-r--r-- 1 pcarlton 2.9K 2019-03-06 16:33:37.666169757 +0900 META.yml
-rw-r--r-- 1 pcarlton 4.3K 2019-03-06 16:33:37.666169757 +0900 META.json
-rw-r--r-- 1 pcarlton 1.2K 2019-03-06 16:33:37.666169757 +0900 MANIFEST.SKIP
-rw-r--r-- 1 pcarlton 2.0K 2019-03-06 16:33:37.666169757 +0900 MANIFEST
-rw-r--r-- 1 pcarlton  12K 2019-03-06 16:33:37.666169757 +0900 LICENSE
drwxr-xr-x 3 pcarlton 4.0K 2019-03-06 16:33:37.666169757 +0900 lib/
-rwxr-xr-x 1 pcarlton 8.6K 2019-03-06 16:33:37.666169757 +0900 INSTALL.pl*
-rw-r--r-- 1 pcarlton 1.2K 2019-03-06 16:33:37.666169757 +0900 DISCLAIMER
-rw-r--r-- 1 pcarlton  164 2019-03-06 16:33:37.666169757 +0900 cpanfile
-rw-r--r-- 1 pcarlton 4.0K 2019-03-06 16:33:37.666169757 +0900 Changes
drwxr-xr-x 2 pcarlton 4.0K 2019-03-06 16:33:37.674169670 +0900 scripts/
-rw-r--r-- 1 pcarlton 171K 2019-03-06 16:33:37.674169670 +0900 ppport.h
drwxr-xr-x 4 pcarlton 4.0K 2019-03-06 16:33:37.758168755 +0900 t/
-rw-r--r-- 1 pcarlton  769 2019-03-06 16:33:37.762168712 +0900 typemap
drwxr-xr-x 2 pcarlton 4.0K 2019-03-06 16:33:37.762168712 +0900 travisci/


(0)[16:34][pcarlton@chromosome-linux:~/code/vagrent/Bio-DB-HTS]
>> perl INSTALL.pl
/home/pcarlton/code/vagrent/Bio-DB-HTS

*** Performing build in /tmp/lT4WhAb5OH ***

*** Checking out HTSlib v1.5 ***
--2019-03-06 16:35:11--  https://github.com/samtools/htslib/archive/1.5.zip
Resolving github.com (github.com)... 192.30.255.113, 192.30.255.112
Connecting to github.com (github.com)|192.30.255.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/samtools/htslib/zip/1.5 [following]
--2019-03-06 16:35:11--  https://codeload.github.com/samtools/htslib/zip/1.5
Resolving codeload.github.com (codeload.github.com)... 192.30.255.121, 192.30.255.120
Connecting to codeload.github.com (codeload.github.com)|192.30.255.121|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: ‘1.5.zip’

1.5.zip                                              [   <=>                                                                                                     ]   1.21M  2.06MB/s    in 0.6s

2019-03-06 16:35:13 (2.06 MB/s) - ‘1.5.zip’ saved [1270304]

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*** Fetching version 2.11 of Bio-DB-HTS from GitHub ***
--2019-03-06 16:35:13--  https://github.com/Ensembl/Bio-DB-HTS/archive/2.11.zip
Resolving github.com (github.com)... 192.30.255.112, 192.30.255.113
Connecting to github.com (github.com)|192.30.255.112|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/Ensembl/Bio-DB-HTS/zip/2.11 [following]
--2019-03-06 16:35:13--  https://codeload.github.com/Ensembl/Bio-DB-HTS/zip/2.11
Resolving codeload.github.com (codeload.github.com)... 192.30.255.120, 192.30.255.121
Connecting to codeload.github.com (codeload.github.com)|192.30.255.120|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: ‘2.11.zip’

2.11.zip                                             [     <=>                                                                                                   ]   4.93M  4.78MB/s    in 1.0s

2019-03-06 16:35:15 (4.78 MB/s) - ‘2.11.zip’ saved [5168760]

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 extracting: Bio-DB-HTS-2.11/t/data/dm3_3R_4766911_4767130.sam.bam
 extracting: Bio-DB-HTS-2.11/t/data/dm3_3R_4766911_4767130.sam.sorted.bam
 extracting: Bio-DB-HTS-2.11/t/data/ex1.bam
  inflating: Bio-DB-HTS-2.11/t/data/ex1.fa
 extracting: Bio-DB-HTS-2.11/t/data/ex1.sam.gz
  inflating: Bio-DB-HTS-2.11/t/data/ex2.bam
 extracting: Bio-DB-HTS-2.11/t/data/ex2.sam.gz
 extracting: Bio-DB-HTS-2.11/t/data/ex3.bam
  inflating: Bio-DB-HTS-2.11/t/data/ex3.bam.csi
  inflating: Bio-DB-HTS-2.11/t/data/no_index.tsv.gz
 extracting: Bio-DB-HTS-2.11/t/data/test.bcf
  inflating: Bio-DB-HTS-2.11/t/data/test.bcf.csi
  inflating: Bio-DB-HTS-2.11/t/data/test.sam
  inflating: Bio-DB-HTS-2.11/t/data/test.tsv.gz
  inflating: Bio-DB-HTS-2.11/t/data/test.tsv.gz.tbi
 extracting: Bio-DB-HTS-2.11/t/data/test.vcf.gz
  inflating: Bio-DB-HTS-2.11/t/data/test.vcf.gz.tbi
  inflating: Bio-DB-HTS-2.11/t/data/yeast.fasta
  inflating: Bio-DB-HTS-2.11/t/data/yeast.sorted.cram
   creating: Bio-DB-HTS-2.11/t/kseq_data/
  inflating: Bio-DB-HTS-2.11/t/kseq_data/bug2335.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/evil_wrapping.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/example.fasta
  inflating: Bio-DB-HTS-2.11/t/kseq_data/example.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/illumina_faked.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/sanger_93.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/sanger_faked.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/solexa_example.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/solexa_faked.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/test1_sanger.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/test2_solexa.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/test3_illumina.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/tricky.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/wrapping_issues.fastq
  inflating: Bio-DB-HTS-2.11/t/kseq_data/zero_qual.fastq
   creating: Bio-DB-HTS-2.11/travisci/
  inflating: Bio-DB-HTS-2.11/travisci/harness.sh
  inflating: Bio-DB-HTS-2.11/typemap

*** Building HTSlib ***
***MAKE***
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.5"' > version.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.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/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico multipart.pico probaln.pico realn.pico regidx.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/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzip.o bgzip.c
gcc  -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o htsfile.o htsfile.c
gcc  -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tabix.o tabix.c
gcc  -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc  -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc  -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/hfile.o test/hfile.c
gcc  -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/sam.o test/sam.c
gcc  -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -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 -lpthread

*** Building Bio::DB::HTS ***
***CMD*** : env HTSLIB_DIR=/tmp/lT4WhAb5OH/htslib perl Build.PL
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.11'
Building Bio-DB-HTS
x86_64-linux-gnu-gcc -I/tmp/lT4WhAb5OH/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
lib/Bio/DB/HTS.xs: In function ‘XS_Bio__DB__HTS__VCF__Header_fmt_text’:
lib/Bio/DB/HTS.xs:1770:5: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
     RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0);
     ^
In file included from lib/Bio/DB/HTS.xs:59:0:
/tmp/lT4WhAb5OH/htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/tmp/lT4WhAb5OH/htslib -Wl,-rpath,/tmp/lT4WhAb5OH/htslib -lhts -lpthread -lz
x86_64-linux-gnu-gcc -I/tmp/lT4WhAb5OH/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/tmp/lT4WhAb5OH/htslib -Wl,-rpath,/tmp/lT4WhAb5OH/htslib -lhts -lpthread -lz
[fai_load] build FASTA index.
[fai_load] build FASTA index.
[fai_load] build FASTA index.
panic: sv_setpvn called with negative strlen -1 at t/07cramwrite.t line 117.
panic: sv_setpvn called with negative strlen -1 at t/08bamwrite.t line 117.
Failed 4/11 test programs. 0/397 subtests failed.
Build test failed. Not continuing at INSTALL.pl line 198.
cannot remove path when cwd is /tmp/lT4WhAb5OH/Bio-DB-HTS for /tmp/lT4WhAb5OH:  at /usr/share/perl/5.22/File/Temp.pm line 778.

## Perl version info

Summary of my perl5 (revision 5 version 22 subversion 1) configuration:
   
  Platform:
    osname=linux, osvers=3.16.0, archname=x86_64-linux-gnu-thread-multi
    uname='linux localhost 3.16.0 #1 smp debian 3.16.0 x86_64 gnulinux '
    config_args='-Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gcc -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDEBIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Dldflags= -Wl,-Bsymbolic-functions -Wl,-z,relro -Dlddlflags=-shared -Wl,-Bsymbolic-functions -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.22 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.22 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.22 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.22.1 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/perl/5.22.1 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -Uversiononly -DDEBUGGING=-g -Doptimize=-O2 -dEs -Duseshrplib -Dlibperl=libperl.so.5.22.1'
    hint=recommended, useposix=true, d_sigaction=define
    useithreads=define, usemultiplicity=define
    use64bitint=define, use64bitall=define, uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='x86_64-linux-gnu-gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2 -g',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include'
    ccversion='', gccversion='5.4.0 20160609', gccosandvers=''
    intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678, doublekind=3
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16, longdblkind=3
    ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=8, prototype=define
  Linker and Libraries:
    ld='x86_64-linux-gnu-gcc', ldflags =' -fstack-protector-strong -L/usr/local/lib'
    libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
    libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt
    perllibs=-ldl -lm -lpthread -lc -lcrypt
    libc=libc-2.23.so, so=so, useshrplib=true, libperl=libperl.so.5.22
    gnulibc_version='2.23'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
    cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector-strong'


Characteristics of this binary (from libperl): 
  Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
                        PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
                        PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
                        USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS
                        USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
                        USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME
                        USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
  Locally applied patches:
	DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN.
	DEBPKG:debian/db_file_ver - http://bugs.debian.org/340047 Remove overly restrictive DB_File version check.
	DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information.
	DEBPKG:debian/enc2xs_inc - http://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @INC directories.
	DEBPKG:debian/errno_ver - http://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes.
	DEBPKG:debian/libperl_embed_doc - http://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking
	DEBPKG:fixes/respect_umask - Respect umask during installation
	DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories
	DEBPKG:debian/extutils_set_libperl_path - EU:MM: set location of libperl.a under /usr/lib
	DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor
	DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets.
	DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor.
	DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy.
	DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable.
	DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian
	DEBPKG:debian/prune_libs - http://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need.
	DEBPKG:fixes/net_smtp_docs - [rt.cpan.org #36038] http://bugs.debian.org/100195 Document the Net::SMTP 'Port' option
	DEBPKG:debian/perlivp - http://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local
	DEBPKG:debian/deprecate-with-apt - http://bugs.debian.org/747628 Point users to Debian packages of deprecated core modules
	DEBPKG:debian/squelch-locale-warnings - http://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts
	DEBPKG:debian/skip-upstream-git-tests - Skip tests specific to the upstream Git repository
	DEBPKG:debian/patchlevel - http://bugs.debian.org/567489 List packaged patches for 5.22.1-9ubuntu0.6 in patchlevel.h
	DEBPKG:debian/skip-kfreebsd-crash - http://bugs.debian.org/628493 [perl #96272] Skip a crashing test case in t/op/threads.t on GNU/kFreeBSD
	DEBPKG:fixes/document_makemaker_ccflags - http://bugs.debian.org/628522 [rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags}
	DEBPKG:debian/find_html2text - http://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text
	DEBPKG:debian/perl5db-x-terminal-emulator.patch - http://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl
	DEBPKG:debian/cpan-missing-site-dirs - http://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable
	DEBPKG:fixes/memoize_storable_nstore - [rt.cpan.org #77790] http://bugs.debian.org/587650 Memoize::Storable: respect 'nstore' option not respected
	DEBPKG:debian/regen-skip - Skip a regeneration check in unrelated git repositories
	DEBPKG:debian/makemaker-pasthru - http://bugs.debian.org/758471 Pass LD settings through to subdirectories
	DEBPKG:fixes/pod_man_reproducible_date - http://bugs.debian.org/759405 Support POD_MAN_DATE in Pod::Man for the left-hand footer
	DEBPKG:debian/locale-robustness - http://bugs.debian.org/782068 [perl #124310] Make t/run/locale.t survive missing locales masked by LC_ALL
	DEBPKG:fixes/podman-utc - http://bugs.debian.org/780259 Make the embedded date from Pod::Man reproducible
	DEBPKG:fixes/podman-utc-docs - http://bugs.debian.org/780259 Documentation and test suite updates for UTC fix
	DEBPKG:fixes/podman-empty-date - http://bugs.debian.org/780259 Support an empty POD_MAN_DATE environment variable
	DEBPKG:fixes/podman-pipe - http://bugs.debian.org/777405 Better errors for man pages from standard input
	DEBPKG:debian/pod2man-customized - Update porting/customized.dat for pod2man modifications
	DEBPKG:debian/makemaker-manext - http://bugs.debian.org/247370 Make EU::MakeMaker honour MANnEXT settings in generated manpage headers
	DEBPKG:debian/makemaker_customized - Update t/porting/customized.dat for files patched in Debian
	DEBPKG:debian/do-not-record-build-date - [6baa8db] http://bugs.debian.org/774422 [perl #125830] Allow overriding the compile time in "perl -V" output
	DEBPKG:fixes/podman-source-date-epoch - http://bugs.debian.org/801621 Make Pod::Man honor the SOURCE_DATE_EPOCH environment variable
	DEBPKG:fixes/podman-source-date-epoch-cleanups - http://bugs.debian.org/801621 Coding style and documentation for SOURCE_EPOCH_DATE
	DEBPKG:fixes/podman-source-date-epoch-testfix - http://bugs.debian.org/807086 Guard for building with SOURCE_DATE_EPOCH or POD_MAN_DATE set
	DEBPKG:debian/devel-ppport-reproducibility - http://bugs.debian.org/801523 Sort the list of XS code files when generating RealPPPort.xs
	DEBPKG:fixes/encode-unicode-bom - http://bugs.debian.org/798727 [rt.cpan.org #107043] Address https://rt.cpan.org/Public/Bug/Display.html?id=107043
	DEBPKG:debian/encode-unicode-bom-doc - http://bugs.debian.org/798727 Document Debian backport of Encode::Unicode fix
	DEBPKG:debian/kfreebsd-softupdates - http://bugs.debian.org/796798 Work around Debian Bug#796798
	DEBPKG:fixes/autodie-scope - http://bugs.debian.org/798096 Fix a scoping issue with "no autodie" and the "system" sub
	DEBPKG:debian/debugperl-compat-fix - [perl #127212] http://bugs.debian.org/810326 Disable PERL_TRACK_MEMPOOL for debugging builds
	DEBPKG:fixes/CVE-2015-8607_file_spec_taint_fix - http://bugs.debian.org/810719 [perl #126862] ensure File::Spec::canonpath() preserves taint
	DEBPKG:fixes/mkstemp-umask - http://bugs.debian.org/810924 [perl #127322] [e57270b] Fix umask for mkstemp(3) calls
	DEBPKG:fixes/crosscompile-no-targethost - [perl #127234] Fix the Configure escape with usecrosscompile but no targethost
	DEBPKG:fixes/podlators-no-encode - [rt.cpan.org #111156] Degrade gracefully if utf8 is requested but Encode is not available
	DEBPKG:debian/cross-time-hires - [rt.cpan.org #111391] Add an environment variable to skip running configuration probes
	DEBPKG:fixes/encode-unicode-pod - Unicode.pm: Fix POD error
	DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in Memoize
	DEBPKG:fixes/ok-pod - Added encoding for pod.
	DEBPKG:fixes/CVE-2016-2381_duplicate_env - remove duplicate environment variables from environ
	DEBPKG:fixes/CVE-2017-12837.patch - [PATCH] regcomp [perl #131582]
	DEBPKG:fixes/CVE-2017-12883.patch - [PATCH] PATCH: [perl #131598]
	DEBPKG:fixes/CVE-2016-6185.patch - [PATCH] =?utf8?q?Don=E2=80=99t=20let=20XSLoader=20load=20relative?= =?utf8?q?=20paths?=
	DEBPKG:fixes/CVE-2017-6512-pre.patch - [PATCH] Correct the order of tests of chmod(). (#294)
	DEBPKG:fixes/CVE-2017-6512.patch - http://bugs.debian.org/863870 [rt.cpan.org #121951] Prevent directory chmod race attack.
	DEBPKG:fixes/CVE-2018-6797.patch - (perl #132227) restart a node if we change to uni rules within the node and encounter a sharp S
	DEBPKG:fixes/CVE-2018-6798-1.patch - [perl #132063]: Heap buffer overflow
	DEBPKG:fixes/CVE-2018-6798-2.patch - v5.24.3: fix TRIE_READ_CHAR and DECL_TRIE_TYPE to account for non-utf8 target
	DEBPKG:fixes/CVE-2018-6798-3.patch - (perl #132063) we should no longer warn for this code
	DEBPKG:fixes/CVE-2018-6913.patch - (perl #131844) fix various space calculation issues in pp_pack.c
	DEBPKG:fixes/CVE-2018-12015.patch - [PATCH] [PATCH] Remove existing files before overwriting them
	DEBPKG:fixes/CVE-2018-18311.patch - [PATCH] Perl_my_setenv(); handle integer wrap
	DEBPKG:fixes/CVE-2018-18312.patch - [PATCH 242/242] PATCH: [perl #133423] for 5.26 maint
	DEBPKG:fixes/CVE-2018-18313.patch - [PATCH] regcomp.c: Convert some strchr to memchr
	DEBPKG:fixes/CVE-2018-18314.patch - [PATCH] fix #131649 - extended charclass can trigger assert
  Built under linux
  Compiled at Nov 19 2018 18:29:35
  %ENV:
    PERL5LIB="/opt/lib/perl5"
    PERLBREW_BASHRC_VERSION="0.78"
    PERLBREW_HOME="/home/pcarlton/.perlbrew"
    PERLBREW_MANPATH="/home/pcarlton/perl5/perlbrew/perls/perl-5.24.1/man"
    PERLBREW_PATH="/home/pcarlton/perl5/perlbrew/bin:/home/pcarlton/perl5/perlbrew/perls/perl-5.24.1/bin"
    PERLBREW_PERL="perl-5.24.1"
    PERLBREW_ROOT="/home/pcarlton/perl5/perlbrew"
    PERLBREW_VERSION="0.78"
  @INC:
    /opt/lib/perl5/x86_64-linux-gnu-thread-multi
    /opt/lib/perl5
    /etc/perl
    /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
    /usr/local/share/perl/5.22.1
    /usr/lib/x86_64-linux-gnu/perl5/5.22
    /usr/share/perl5
    /usr/lib/x86_64-linux-gnu/perl/5.22
    /usr/share/perl/5.22
    /usr/local/lib/site_perl
    /usr/lib/x86_64-linux-gnu/perl-base
    .