[package - head-amd64-default][biology/iolib] Failed for io_lib-1.14.10 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Mar 24 05:56:21 UTC 2019
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: danilo at FreeBSD.org
Last committer: linimon at FreeBSD.org
Ident: $FreeBSD: head/biology/iolib/Makefile 484209 2018-11-05 19:42:37Z linimon $
Log URL: http://beefy12.nyi.freebsd.org/data/head-amd64-default/p496699_s345461/logs/io_lib-1.14.10.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p496699_s345461
Log:
=>> Building biology/iolib
build started at Sun Mar 24 05:54:22 UTC 2019
port directory: /usr/ports/biology/iolib
package name: io_lib-1.14.10
building for: FreeBSD head-amd64-default-job-16 13.0-CURRENT FreeBSD 13.0-CURRENT 1300017 amd64
maintained by: danilo at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/iolib/Makefile 484209 2018-11-05 19:42:37Z linimon $
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!!! This is not supported. !!!
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!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[head-amd64-default-job-16] Installing pkg-1.10.5_5...
[head-amd64-default-job-16] Extracting pkg-1.10.5_5: .......... done
===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of io_lib-1.14.10
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by io_lib-1.14.10 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by io_lib-1.14.10 for building
=> SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by io_lib-1.14.10 for building
===> Extracting for io_lib-1.14.10
=> SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for io_lib-1.14.10
===> Applying FreeBSD patches for io_lib-1.14.10
===========================================================================
=======================<phase: build-depends >============================
===> io_lib-1.14.10 depends on package: autoconf>=2.69 - not found
===> Installing existing package /packages/All/autoconf-2.69_2.txz
[head-amd64-default-job-16] Installing autoconf-2.69_2...
<snip>
mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo
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libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c
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libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c
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libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1
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/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c -o libstaden_read_la-rANS_static.lo `test -f 'rANS_static.c' || echo './'`rANS_static.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static.o
rANS_static.c:274:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function]
static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq)
^
rANS_static.c:318:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function]
static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits)
^
rANS_static.c:336:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function]
static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits)
^
rANS_static.c:348:20: warning: unused function 'RansDecRenorm' [-Wunused-function]
static inline void RansDecRenorm(RansState* r, uint8_t** pptr) {
^
rANS_static.c:470:20: warning: unused function 'RansDecAdvanceSymbol32' [-Wunused-function]
static inline void RansDecAdvanceSymbol32(RansState* r, uint8_t** pptr, RansDecSymbol32 const* sym, uint32_t scale_bits)
^
5 warnings generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -o libstaden_read_la-rANS_static.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-rANS_static.Tpo .deps/libstaden_read_la-rANS_static.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c -o libstaden_read_la-rANS_static4x16pr.lo `test -f 'rANS_static4x16pr.c' || echo './'`rANS_static4x16pr.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static4x16pr.o
rANS_static4x16pr.c:107:20: warning: unused function 'RansEncPut' [-Wunused-function]
static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits)
^
rANS_static4x16pr.c:149:24: warning: unused function 'RansDecGet' [-Wunused-function]
static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits)
^
rANS_static4x16pr.c:282:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function]
static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq)
^
rANS_static4x16pr.c:334:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function]
static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits)
^
rANS_static4x16pr.c:352:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function]
static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits)
^
5 warnings generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -o libstaden_read_la-rANS_static4x16pr.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-rANS_static4x16pr.Tpo .deps/libstaden_read_la-rANS_static4x16pr.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o
cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^~~~~~~~~~~~~~~~
./cram_io.h:105:311: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
~~~~~^~~~~~~~~~~~~~~~~
cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^~~~~~~~~~~~~~~~
./cram_io.h:105:345: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
~~~~~~~~~~^~~~~
cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^~~~~~~~~~~~~~~~
./cram_io.h:105:367: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
~~~~~~~~~~^~~~~
cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion]
cp += itf8_put(cp, -2);
^~~~~~~~~~~~~~~~
./cram_io.h:105:388: note: expanded from macro 'itf8_put'
#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
~~~~~~~~~^~~~~
4 warnings generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c -o libstaden_read_la-tokenise_name3.lo `test -f 'tokenise_name3.c' || echo './'`tokenise_name3.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o .libs/libstaden_read_la-tokenise_name3.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -o libstaden_read_la-tokenise_name3.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-tokenise_name3.Tpo .deps/libstaden_read_la-tokenise_name3.Plo
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c -o libstaden_read_la-fqzcomp_qual.lo `test -f 'fqzcomp_qual.c' || echo './'`fqzcomp_qual.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o .libs/libstaden_read_la-fqzcomp_qual.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -o libstaden_read_la-fqzcomp_qual.o >/dev/null 2>&1
mv -f .deps/libstaden_read_la-fqzcomp_qual.Tpo .deps/libstaden_read_la-fqzcomp_qual.Plo
/bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -version-info 13:0:0 -fstack-protector -o libstaden-read.la -rpath /usr/local/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo l
ibstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-rANS_static.lo libstaden_read_la-rANS_static4x16pr.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo libstaden_read_la-tokenise_name3.lo libstaden_read_la-fqzcomp_qual.lo -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2
libtool: link: cc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstade
n_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-rANS_static.o .libs/libstaden_read_la-rANS_static4x16pr.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o .libs/libstaden_read_la-tokenise_name3.o .libs/libstaden_read_la-fqzcomp_qual.o -lz
-L/usr/local/lib -lcurl -lm -llzma -lbz2 -O!
2 -fstack-protector -fstack-protector -Wl,-soname -Wl,libstaden-read.so.13 -o .libs/libstaden-read.so.13.0.0
libtool: link: (cd ".libs" && rm -f "libstaden-read.so.13" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so.13")
libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so")
libtool: link: ar cru .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_
alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-rANS_static.o libstaden_read_la-rANS_static4x16pr.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libstaden_read_la-tokenise_name3.o libstaden_read_la-fqzcomp_qual.o
libtool: link: ranlib .libs/libstaden-read.a
libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" )
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib'
Making all in progs
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs'
cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c
mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po
/bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -fstack-protector -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -fstack-protector -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib
ld: error: ../io_lib/.libs/libstaden-read.so: undefined reference to pthread_create
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[3]: *** [Makefile:644: convert_trace] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs'
gmake[2]: *** [Makefile:750: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10'
gmake[1]: *** [Makefile:495: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/iolib
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