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 = $(TOUCH) LN_S = @LN_S@ GREP = @GREP@ --- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800 +++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800 @@ -10417,10 +10417,6 @@ echo "${ECHO_T}no, using $LN_S" >&6; } fi -case "$LN_S" in - /*) ;; - * ) LN_S=/bin/$LN_S ;; -esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.