[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_i386_12 #34216
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Thu Feb 16 06:23:20 UTC 2017
https://jenkins.debian.net/job/reproducible_builder_i386_12/34216/------------------------------------------
[...truncated 391.87 KB...]
#warning \
^~~~~~~
-libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o
+libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o
dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO':
dmSML/aPOSIXaio.c:115:21: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types]
rval = aio_suspend(request_array, 1, &zero_wait);
@@ -775,18 +786,18 @@
/usr/include/aio.h:199:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **'
extern int __REDIRECT_NTH (aio_suspend,
^
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o
dmSML/util.c: In function 'removeFile':
dmSML/util.c:126:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
rm_cmd = Fmt( "/bin/rm -fv %s", filename );
@@ -797,20 +808,20 @@
dmSML/util.c:129:16: warning: implicit declaration of function 'system' [-Wimplicit-function-declaration]
return system( rm_cmd );
^~~~~~
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o
-libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1
-/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/build/1st/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems-1.6.la -rpath /usr/lib/i386-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome-1.3 -lMUSCLE-3.7 -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o
+libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1
+/bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/build/2nd/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems-1.6.la -rpath /usr/lib/i386-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome-1.3 -lMUSCLE-3.7 -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/6/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/6/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome-1.3 -lMUSCLE-3.7 -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/i686-linux-gnu/6 -L/usr/lib/gcc/i686-linux-gnu/6/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/6/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/6/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/6/crtendS.o /usr/lib/gcc/i686-linux-gnu/6/../../../i386-linux-gnu/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems-1.6.so.1 -o .libs/libMems-1.6.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libMems-1.6.so.1" && ln -s "libMems-1.6.so.1.0.0" "libMems-1.6.so.1")
libtool: link: (cd ".libs" && rm -f "libMems-1.6.so" && ln -s "libMems-1.6.so.1.0.0" "libMems-1.6.so")
@@ -818,21 +829,21 @@
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libMems-1.6.a
libtool: link: ( cd ".libs" && rm -f "libMems-1.6.la" && ln -s "../libMems-1.6.la" "libMems-1.6.la" )
-make[3]: Leaving directory '/build/1st/libmems-1.6.0+4725/libMems'
-make[3]: Entering directory '/build/1st/libmems-1.6.0+4725'
-make[3]: Leaving directory '/build/1st/libmems-1.6.0+4725'
-make[2]: Leaving directory '/build/1st/libmems-1.6.0+4725'
-make[1]: Leaving directory '/build/1st/libmems-1.6.0+4725'
+make[3]: Leaving directory '/build/2nd/libmems-1.6.0+4725/libMems'
+make[3]: Entering directory '/build/2nd/libmems-1.6.0+4725'
+make[3]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
+make[2]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
+make[1]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
dh_auto_test
make -j1 check VERBOSE=1
-make[1]: Entering directory '/build/1st/libmems-1.6.0+4725'
+make[1]: Entering directory '/build/2nd/libmems-1.6.0+4725'
Making check in libMems
-make[2]: Entering directory '/build/1st/libmems-1.6.0+4725/libMems'
+make[2]: Entering directory '/build/2nd/libmems-1.6.0+4725/libMems'
make[2]: Nothing to be done for 'check'.
-make[2]: Leaving directory '/build/1st/libmems-1.6.0+4725/libMems'
-make[2]: Entering directory '/build/1st/libmems-1.6.0+4725'
-make[2]: Leaving directory '/build/1st/libmems-1.6.0+4725'
-make[1]: Leaving directory '/build/1st/libmems-1.6.0+4725'
+make[2]: Leaving directory '/build/2nd/libmems-1.6.0+4725/libMems'
+make[2]: Entering directory '/build/2nd/libmems-1.6.0+4725'
+make[2]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
+make[1]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary --with autoreconf
@@ -840,40 +851,40 @@
dh_testroot
dh_prep
dh_auto_install
- make -j1 install DESTDIR=/build/1st/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no
-make[1]: Entering directory '/build/1st/libmems-1.6.0+4725'
+ make -j1 install DESTDIR=/build/2nd/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no
+make[1]: Entering directory '/build/2nd/libmems-1.6.0+4725'
Making install in libMems
-make[2]: Entering directory '/build/1st/libmems-1.6.0+4725/libMems'
-make[3]: Entering directory '/build/1st/libmems-1.6.0+4725/libMems'
- /bin/mkdir -p '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu'
- /bin/bash ../libtool --mode=install /usr/bin/install -c libMems-1.6.la '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu'
-libtool: install: /usr/bin/install -c .libs/libMems-1.6.so.1.0.0 /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1.0.0
-libtool: install: (cd /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so.1 || { rm -f libMems-1.6.so.1 && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so.1; }; })
-libtool: install: (cd /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so || { rm -f libMems-1.6.so && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so; }; })
-libtool: install: /usr/bin/install -c .libs/libMems-1.6.lai /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.la
-libtool: install: /usr/bin/install -c .libs/libMems-1.6.a /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
-libtool: install: chmod 644 /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
-libtool: install: ranlib /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
+make[2]: Entering directory '/build/2nd/libmems-1.6.0+4725/libMems'
+make[3]: Entering directory '/build/2nd/libmems-1.6.0+4725/libMems'
+ /bin/mkdir -p '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu'
+ /bin/sh ../libtool --mode=install /usr/bin/install -c libMems-1.6.la '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu'
+libtool: install: /usr/bin/install -c .libs/libMems-1.6.so.1.0.0 /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1.0.0
+libtool: install: (cd /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so.1 || { rm -f libMems-1.6.so.1 && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so.1; }; })
+libtool: install: (cd /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so || { rm -f libMems-1.6.so && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so; }; })
+libtool: install: /usr/bin/install -c .libs/libMems-1.6.lai /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.la
+libtool: install: /usr/bin/install -c .libs/libMems-1.6.a /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
+libtool: install: chmod 644 /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
+libtool: install: ranlib /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a
libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu'
- /bin/mkdir -p '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML'
- /usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML'
- /bin/mkdir -p '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM'
- /usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM'
- /bin/mkdir -p '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
- /usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
- /usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
-make[3]: Leaving directory '/build/1st/libmems-1.6.0+4725/libMems'
-make[2]: Leaving directory '/build/1st/libmems-1.6.0+4725/libMems'
-make[2]: Entering directory '/build/1st/libmems-1.6.0+4725'
-make[3]: Entering directory '/build/1st/libmems-1.6.0+4725'
+ /bin/mkdir -p '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML'
+ /usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML'
+ /bin/mkdir -p '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM'
+ /usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM'
+ /bin/mkdir -p '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
+ /usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
+ /usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems'
+make[3]: Leaving directory '/build/2nd/libmems-1.6.0+4725/libMems'
+make[2]: Leaving directory '/build/2nd/libmems-1.6.0+4725/libMems'
+make[2]: Entering directory '/build/2nd/libmems-1.6.0+4725'
+make[3]: Entering directory '/build/2nd/libmems-1.6.0+4725'
make[3]: Nothing to be done for 'install-exec-am'.
- /bin/mkdir -p '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
- /usr/bin/install -c -m 644 libMems-1.6.pc '/build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
-make[3]: Leaving directory '/build/1st/libmems-1.6.0+4725'
-make[2]: Leaving directory '/build/1st/libmems-1.6.0+4725'
-make[1]: Leaving directory '/build/1st/libmems-1.6.0+4725'
+ /bin/mkdir -p '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
+ /usr/bin/install -c -m 644 libMems-1.6.pc '/build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig'
+make[3]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
+make[2]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
+make[1]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
debian/rules override_dh_install
-make[1]: Entering directory '/build/1st/libmems-1.6.0+4725'
+make[1]: Entering directory '/build/2nd/libmems-1.6.0+4725'
dh_install
d-shlibmove --commit \
--multiarch \
@@ -894,15 +905,15 @@
install -d -m 755 debian/libmems-1.6-1v5/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.a debian/libmems-1.6-dev/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so debian/libmems-1.6-dev/usr/lib/i386-linux-gnu
-mv /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1 debian/libmems-1.6-1v5/usr/lib/i386-linux-gnu
-mv /build/1st/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1.0.0 debian/libmems-1.6-1v5/usr/lib/i386-linux-gnu
+mv /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1 debian/libmems-1.6-1v5/usr/lib/i386-linux-gnu
+mv /build/2nd/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems-1.6.so.1.0.0 debian/libmems-1.6-1v5/usr/lib/i386-linux-gnu
PKGDEV=libmems-1.6-dev
PKGSHL=libmems-1.6-1v5
install -d -m 755 debian/libmems-1.6-dev/usr
mv debian/tmp/usr/include debian/libmems-1.6-dev/usr
install -d -m 755 debian/libmems-1.6-dev/usr/lib/i386-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-1.6-dev/usr/lib/i386-linux-gnu/pkgconfig
-make[1]: Leaving directory '/build/1st/libmems-1.6.0+4725'
+make[1]: Leaving directory '/build/2nd/libmems-1.6.0+4725'
dh_installdocs
dh_installchangelogs
dh_perl
@@ -917,8 +928,8 @@
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'libmems-1.6-dev' in '../libmems-1.6-dev_1.6.0+4725-4_i386.deb'.
dpkg-deb: building package 'libmems-1.6-1v5-dbgsym' in '../libmems-1.6-1v5-dbgsym_1.6.0+4725-4_i386.deb'.
+dpkg-deb: building package 'libmems-1.6-dev' in '../libmems-1.6-dev_1.6.0+4725-4_i386.deb'.
dpkg-deb: building package 'libmems-1.6-1v5' in '../libmems-1.6-1v5_1.6.0+4725-4_i386.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../libmems_1.6.0+4725-4_i386.changes
@@ -926,12 +937,14 @@
dpkg-source --after-build libmems-1.6.0+4725
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/12745/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/12745/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/17855 and its subdirectories
-I: Current time: Wed Mar 21 00:32:50 -12 2018
-I: pbuilder-time-stamp: 1521635570
+I: removing directory /srv/workspace/pbuilder/12745 and its subdirectories
+I: Current time: Thu Feb 16 20:23:17 +14 2017
+I: pbuilder-time-stamp: 1487226197
Starting cleanup.
/srv/reproducible-results/rbuild-debian-HaheeDQb/tmp.XaUSLzvhkK: 85.7% -- replaced with /srv/reproducible-results/rbuild-debian-HaheeDQb/tmp.XaUSLzvhkK.gz
INFO: Starting at 2017-02-16 06:23:19.288037
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/i386/libmems_1.6.0+4725-4_i386.buildinfo
CRITICAL: https://tests.reproducible-builds.org/debian/unstable/i386/libmems didn't produce a buildlog, even though it has been built.
INFO: Finished at 2017-02-16 06:23:19.790191, took: 0:00:00.502168
All cleanup done.
Thu 16 Feb 06:23:20 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-08KTcuNo, which will now be removed.
Build step 'Execute shell' marked build as failure
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