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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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800
@@ -1,8 +1,5 @@
#!/bin/sh
set -e
-PATH=/bin:/usr/bin
-export PATH
-unset CDPATH
base=$1
search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '`
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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800
@@ -1,9 +1,6 @@
#!/bin/sh
id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $'
-PATH=/bin:/usr/bin
-export PATH
-
exec > auto_flat_tuneups.mk
cat <<EOF
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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800
@@ -1,7 +1,5 @@
#!/bin/sh
-PATH=/bin:/usr/bin
-export PATH
dir=$1.lock
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800
@@ -4,9 +4,6 @@
# Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov)
#################################
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-
script_name=`basename $0`
script_args="$*"
@@ -16,7 +13,7 @@
base_action=`basename "$action"`
case "$base_action" in
cp | cp\ * | ln | ln\ * )
- action=/bin/$base_action
+ action=$base_action
rm="rm -f"
;;
* )
@@ -58,10 +55,8 @@
shift
cmd="$* $dest_file"
test "$quiet" = yes || echo "$cmd"
- PATH=$orig_PATH
"$@" "$dest"
status=$?
- PATH=/bin:/usr/bin
return $status
}
@@ -74,7 +69,7 @@
case "$base_action" in
ln | ln\ -f )
test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead"
- cmd="/bin/cp -p $src_file $dest_file"
+ cmd="cp -p $src_file $dest_file"
ExecHelper "$dest_file" /bin/cp -p "$src_file" ||
Usage "\"$cmd\" failed"
;;
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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800
@@ -1,8 +1,6 @@
#!/bin/sh
# $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $
-PATH=/bin:/usr/bin
-export PATH
act=false
cache_dir='.#SRC-cache'
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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800
@@ -1,10 +1,6 @@
#!/bin/sh
# $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-export PATH
-
base=
logfile=
map=
@@ -23,7 +19,7 @@
: ${base:=`basename "$1"`}
clean_up () {
- /bin/rm -rf "$base.lock"
+ rm -rf "$base.lock"
}
case $0 in
@@ -45,7 +41,7 @@
trap "clean_up; exit $error_status" 1 2 15
if [ -n "$logfile" ]; then
status_file=$base.lock/status
- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \
+ ("$@"; echo $? > "$status_file") 2>&1 \
| tee "$logfile.new"
# Emulate egrep -q to avoid having to move from under scripts.
if [ ! -f "$logfile" ] \
@@ -58,8 +54,6 @@
status=1
fi
else
- PATH=$orig_PATH
- export PATH
"$@"
status=$?
fi
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
--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800
@@ -1,8 +1,5 @@
#!/bin/sh
-PATH=/bin:/usr/bin:/usr/ccs/bin
-export PATH
-
case "$1" in
--dirs )
shift
--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800
@@ -1,6 +1,4 @@
#!/bin/sh
-PATH=/bin:/usr/bin
-export PATH
script_name=`basename $0`
script_dir=`dirname $0`
--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800
@@ -50,12 +50,12 @@
### Auxiliary commands, filters
-RM = /bin/rm -f
-RMDIR = /bin/rm -rf
-COPY = /bin/cp -p
+RM = rm -f
+RMDIR = rm -rf
+COPY = cp -p
BINCOPY = @BINCOPY@
TOUCH = @TOUCH@
-MKDIR = /bin/mkdir
+MKDIR = mkdir
BINTOUCH = $(TOUCH)
LN_S = @LN_S@
GREP = @GREP@
--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800
@@ -10417,4 +10417,0 @@
-case "$LN_S" in
- /*) ;;
- * ) LN_S=/bin/$LN_S ;;
-esac
|