184 lines
6.1 KiB
Diff
184 lines
6.1 KiB
Diff
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800
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@@ -1,8 +1,5 @@
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#!/bin/sh
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set -e
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-PATH=/bin:/usr/bin
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-export PATH
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-unset CDPATH
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base=$1
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search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '`
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800
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@@ -1,9 +1,6 @@
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#!/bin/sh
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id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $'
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-PATH=/bin:/usr/bin
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-export PATH
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-
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exec > auto_flat_tuneups.mk
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cat <<EOF
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800
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@@ -1,7 +1,5 @@
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#!/bin/sh
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-PATH=/bin:/usr/bin
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-export PATH
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dir=$1.lock
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800
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@@ -4,9 +4,6 @@
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# Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov)
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#################################
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-orig_PATH=$PATH
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-PATH=/bin:/usr/bin
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-
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script_name=`basename $0`
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script_args="$*"
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@@ -16,7 +13,7 @@
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base_action=`basename "$action"`
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case "$base_action" in
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cp | cp\ * | ln | ln\ * )
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- action=/bin/$base_action
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+ action=$base_action
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rm="rm -f"
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;;
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* )
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@@ -58,10 +55,8 @@
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shift
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cmd="$* $dest_file"
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test "$quiet" = yes || echo "$cmd"
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- PATH=$orig_PATH
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"$@" "$dest"
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status=$?
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- PATH=/bin:/usr/bin
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return $status
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}
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@@ -74,7 +69,7 @@
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case "$base_action" in
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ln | ln\ -f )
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test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead"
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- cmd="/bin/cp -p $src_file $dest_file"
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+ cmd="cp -p $src_file $dest_file"
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ExecHelper "$dest_file" /bin/cp -p "$src_file" ||
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Usage "\"$cmd\" failed"
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;;
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800
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@@ -1,8 +1,6 @@
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#!/bin/sh
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# $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $
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-PATH=/bin:/usr/bin
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-export PATH
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act=false
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cache_dir='.#SRC-cache'
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800
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@@ -1,10 +1,6 @@
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#!/bin/sh
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# $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $
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-orig_PATH=$PATH
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-PATH=/bin:/usr/bin
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-export PATH
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-
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base=
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logfile=
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map=
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@@ -23,7 +19,7 @@
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: ${base:=`basename "$1"`}
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clean_up () {
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- /bin/rm -rf "$base.lock"
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+ rm -rf "$base.lock"
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}
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case $0 in
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@@ -45,7 +41,7 @@
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trap "clean_up; exit $error_status" 1 2 15
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if [ -n "$logfile" ]; then
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status_file=$base.lock/status
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- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \
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+ ("$@"; echo $? > "$status_file") 2>&1 \
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| tee "$logfile.new"
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# Emulate egrep -q to avoid having to move from under scripts.
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if [ ! -f "$logfile" ] \
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@@ -58,8 +54,6 @@
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status=1
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fi
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else
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- PATH=$orig_PATH
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- export PATH
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"$@"
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status=$?
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fi
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diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800
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@@ -1,8 +1,5 @@
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#!/bin/sh
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-PATH=/bin:/usr/bin:/usr/ccs/bin
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-export PATH
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-
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case "$1" in
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--dirs )
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shift
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--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800
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@@ -1,6 +1,4 @@
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#!/bin/sh
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-PATH=/bin:/usr/bin
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-export PATH
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script_name=`basename $0`
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script_dir=`dirname $0`
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--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800
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@@ -50,12 +50,12 @@
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### Auxiliary commands, filters
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-RM = /bin/rm -f
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-RMDIR = /bin/rm -rf
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-COPY = /bin/cp -p
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+RM = rm -f
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+RMDIR = rm -rf
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+COPY = cp -p
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BINCOPY = @BINCOPY@
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TOUCH = @TOUCH@
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-MKDIR = /bin/mkdir
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+MKDIR = mkdir
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BINTOUCH = $(TOUCH)
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LN_S = @LN_S@
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GREP = @GREP@
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--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800
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+++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800
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@@ -10417,10 +10417,6 @@
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echo "${ECHO_T}no, using $LN_S" >&6; }
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fi
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-case "$LN_S" in
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- /*) ;;
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- * ) LN_S=/bin/$LN_S ;;
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-esac
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if test -n "$ac_tool_prefix"; then
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# Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
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