mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-11-26 07:31:20 +00:00
185 lines
6.1 KiB
Diff
185 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
|
|
--- 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.
|