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1diff -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
2--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800
3+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800
4@@ -1,8 +1,5 @@
5 #!/bin/sh
6 set -e
7-PATH=/bin:/usr/bin
8-export PATH
9-unset CDPATH
10
11 base=$1
12 search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '`
13diff -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
14--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800
15+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800
16@@ -1,9 +1,6 @@
17 #!/bin/sh
18 id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $'
19
20-PATH=/bin:/usr/bin
21-export PATH
22-
23 exec > auto_flat_tuneups.mk
24
25 cat <<EOF
26diff -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
27--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800
28+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800
29@@ -1,7 +1,5 @@
30 #!/bin/sh
31
32-PATH=/bin:/usr/bin
33-export PATH
34
35 dir=$1.lock
36
37diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh
38--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800
39+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800
40@@ -4,9 +4,6 @@
41 # Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov)
42 #################################
43
44-orig_PATH=$PATH
45-PATH=/bin:/usr/bin
46-
47 script_name=`basename $0`
48 script_args="$*"
49
50@@ -16,7 +13,7 @@
51 base_action=`basename "$action"`
52 case "$base_action" in
53 cp | cp\ * | ln | ln\ * )
54- action=/bin/$base_action
55+ action=$base_action
56 rm="rm -f"
57 ;;
58 * )
59@@ -58,10 +55,8 @@
60 shift
61 cmd="$* $dest_file"
62 test "$quiet" = yes || echo "$cmd"
63- PATH=$orig_PATH
64 "$@" "$dest"
65 status=$?
66- PATH=/bin:/usr/bin
67 return $status
68 }
69
70@@ -74,7 +69,7 @@
71 case "$base_action" in
72 ln | ln\ -f )
73 test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead"
74- cmd="/bin/cp -p $src_file $dest_file"
75+ cmd="cp -p $src_file $dest_file"
76 ExecHelper "$dest_file" /bin/cp -p "$src_file" ||
77 Usage "\"$cmd\" failed"
78 ;;
79diff -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
80--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800
81+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800
82@@ -1,8 +1,6 @@
83 #!/bin/sh
84 # $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $
85
86-PATH=/bin:/usr/bin
87-export PATH
88
89 act=false
90 cache_dir='.#SRC-cache'
91diff -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
92--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800
93+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800
94@@ -1,10 +1,6 @@
95 #!/bin/sh
96 # $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $
97
98-orig_PATH=$PATH
99-PATH=/bin:/usr/bin
100-export PATH
101-
102 base=
103 logfile=
104 map=
105@@ -23,7 +19,7 @@
106 : ${base:=`basename "$1"`}
107
108 clean_up () {
109- /bin/rm -rf "$base.lock"
110+ rm -rf "$base.lock"
111 }
112
113 case $0 in
114@@ -45,7 +41,7 @@
115 trap "clean_up; exit $error_status" 1 2 15
116 if [ -n "$logfile" ]; then
117 status_file=$base.lock/status
118- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \
119+ ("$@"; echo $? > "$status_file") 2>&1 \
120 | tee "$logfile.new"
121 # Emulate egrep -q to avoid having to move from under scripts.
122 if [ ! -f "$logfile" ] \
123@@ -58,8 +54,6 @@
124 status=1
125 fi
126 else
127- PATH=$orig_PATH
128- export PATH
129 "$@"
130 status=$?
131 fi
132diff -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
133--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800
134+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800
135@@ -1,8 +1,5 @@
136 #!/bin/sh
137
138-PATH=/bin:/usr/bin:/usr/ccs/bin
139-export PATH
140-
141 case "$1" in
142 --dirs )
143 shift
144--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800
145+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800
146@@ -1,6 +1,4 @@
147 #!/bin/sh
148-PATH=/bin:/usr/bin
149-export PATH
150
151 script_name=`basename $0`
152 script_dir=`dirname $0`
153--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800
154+++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800
155@@ -50,12 +50,12 @@
156
157 ### Auxiliary commands, filters
158
159-RM = /bin/rm -f
160-RMDIR = /bin/rm -rf
161-COPY = /bin/cp -p
162+RM = rm -f
163+RMDIR = rm -rf
164+COPY = cp -p
165 BINCOPY = @BINCOPY@
166 TOUCH = @TOUCH@
167-MKDIR = /bin/mkdir
168+MKDIR = mkdir
169 BINTOUCH = $(TOUCH)
170 LN_S = @LN_S@
171 GREP = @GREP@
172--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800
173+++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800
174@@ -10417,4 +10417,0 @@
175-case "$LN_S" in
176- /*) ;;
177- * ) LN_S=/bin/$LN_S ;;
178-esac