===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
rsem-1.3.3+dfsg/README.md-67-`prefix` variables. The RSEM executables will be installed to
rsem-1.3.3+dfsg/README.md:68:`${DESTDIR}${prefix}/bin`. The default values of `DESTDIR` and
rsem-1.3.3+dfsg/README.md-69-`prefix` are `DESTDIR=` and `prefix=/usr/local`. For example,
##############################################
rsem-1.3.3+dfsg/pRSEM/idrCode/submit.idrmerge.lsf.sh-46-
rsem-1.3.3+dfsg/pRSEM/idrCode/submit.idrmerge.lsf.sh:47: if [[ `echo ${combFname} | grep -E '\.gz$'` ]]
rsem-1.3.3+dfsg/pRSEM/idrCode/submit.idrmerge.lsf.sh-48- then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-580- cat('Downloading ChIP file:',iparams$chip.file,"\n",file=stdout())
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R:581: if (system(paste('wget -N -q -P',iparams$temp.dir,iparams$chip.file)) != 0) {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-582- stop('Error downloading ChIP file:',iparams$chip.file)
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-590- cat('Downloading control file:',iparams$control.file,"\n",file=stdout())
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R:591: if (system(paste('wget -N -q -P',iparams$temp.dir,iparams$control.file)) != 0) {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-592- stop('Error downloading Control file:',iparams$control.file)
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-862- write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R:863: system(paste('gzip -f ',iparams$output.npeak.file))
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-864- }
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-869- write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R:870: system(paste('gzip -f ',iparams$output.rpeak.file))
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp.R-871- }
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-580- cat('Downloading ChIP file:',iparams$chip.file,"\n",file=stdout())
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R:581: if (system(paste('wget -N -q -P',iparams$temp.dir,iparams$chip.file)) != 0) {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-582- stop('Error downloading ChIP file:',iparams$chip.file)
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-590- cat('Downloading control file:',iparams$control.file,"\n",file=stdout())
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R:591: if (system(paste('wget -N -q -P',iparams$temp.dir,iparams$control.file)) != 0) {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-592- stop('Error downloading Control file:',iparams$control.file)
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-863- write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R:864: system(paste('gzip -f ',iparams$output.npeak.file))
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-865- }
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-870- write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R:871: system(paste('gzip -f ',iparams$output.rpeak.file))
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/run_spp_nodups.R-872- }
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-46-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:47:if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-48- as_echo='printf %s\n'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-50-else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:51: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-52- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-60- expr "X$arg" : "X\\(.*\\)$as_nl";
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:61: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-62- esac;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-234- test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:235: test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-236-") 2> /dev/null; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-349- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:350: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-351-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-445- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:446: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-447-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-558- esac;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:559: case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-560- ???[sx]*):;;*)false;;esac;fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-721- case $ac_option in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:722: *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-723- *) ac_optarg=yes ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-764- -disable-* | --disable-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:765: ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-766- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-770- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:771: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-772- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-791- -enable-* | --enable-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:792: ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-793- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-797- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:798: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-799- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-996- -with-* | --with-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:997: ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-998- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1002- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1003: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1004- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1013- -without-* | --without-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1014: ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1015- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1019- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1020: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1021- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1053- *=*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1054: ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1055- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1073-if test -n "$ac_prev"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1074: ac_option=--`echo $ac_prev | sed 's/_/-/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1075- { $as_echo "$as_me: error: missing argument to $ac_option" >&2
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1097- */ )
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1098: ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1099- eval $ac_var=\$ac_val;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1135-ac_ls_di=`ls -di .` &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1136:ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1137- { $as_echo "$as_me: error: working directory cannot be determined" >&2
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1195-case $srcdir in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1196:*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1197-esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1238-By default, \`make install' will install all the files in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1239:\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1240:an installation prefix other than \`$ac_default_prefix' using \`--prefix',
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1241-for instance \`--prefix=\$HOME'.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1303-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1304: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1305- # A ".." for each directory in $ac_dir_suffix.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1306: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1307- case $ac_top_builddir_sub in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1436- *\'*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1437: ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1438- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1523- case $ac_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1524: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1525- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1540- case $ac_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1541: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1542- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1651- set,)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1652: { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1653:$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1654- ac_cache_corrupted=: ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1662- # differences in whitespace do not lead to failure.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1663: ac_old_val_w=`echo x $ac_old_val`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1664: ac_new_val_w=`echo x $ac_new_val`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1665- if test "$ac_old_val_w" != "$ac_new_val_w"; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1682- case $ac_new_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:1683: *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-1684- *) ac_arg=$ac_var=$ac_new_val ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2099-$as_echo_n "checking for C compiler default output file name... " >&6; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2100:ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2101-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2143- then :; else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2144: ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2145- fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2246- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2247: *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2248- break;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2304- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2305: *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2306- break;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2860-'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2861:DEFS=`sed -n "$ac_script" confdefs.h`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2862-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2868- ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2869: ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2870- # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2938-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2939:if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2940- as_echo='printf %s\n'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2942-else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2943: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2944- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2952- expr "X$arg" : "X\\(.*\\)$as_nl";
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:2953: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-2954- esac;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3068- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3069: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3070-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3181- esac;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3182: case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3183- ???[sx]*):;;*)false;;esac;fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3253-configured by $0, generated by GNU Autoconf 2.63,
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3254: with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3255-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3271- --*=*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3272: ac_option=`expr "X$1" : 'X\([^=]*\)='`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3273: ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3274- ac_shift=:
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3293- case $ac_optarg in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3294: *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3295- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3407-ac_cr=''
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3408:ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3409-if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3426- { (exit 1); exit 1; }; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3427:ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3428-ac_delim='%!_!# '
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3434-
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3435: ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3436- if test $ac_delim_n = $ac_delim_num; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3596- esac
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3597: case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3598- ac_file_inputs="$ac_file_inputs '$ac_f'"
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3659- case $as_dir in #(
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3660: *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3661- *) as_qdir=$as_dir;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3697-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3698: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3699- # A ".." for each directory in $ac_dir_suffix.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3700: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3701- case $ac_top_builddir_sub in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3751-'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3752:case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3753-*datarootdir*) ac_datarootdir_seen=yes;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3768-
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3769:# Neutralize VPATH when `$srcdir' = `.'.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3770-# Shell code in configure.ac might set extrasub.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3796-test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3797: { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure:3798: { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/configure-3799- { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-46-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:47:if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-48- as_echo='printf %s\n'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-50-else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:51: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-52- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-60- expr "X$arg" : "X\\(.*\\)$as_nl";
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:61: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-62- esac;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-234- test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:235: test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-236-") 2> /dev/null; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-349- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:350: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-351-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-445- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:446: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-447-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-558- esac;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:559: case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-560- ???[sx]*):;;*)false;;esac;fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-721- case $ac_option in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:722: *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-723- *) ac_optarg=yes ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-764- -disable-* | --disable-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:765: ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-766- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-770- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:771: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-772- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-791- -enable-* | --enable-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:792: ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-793- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-797- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:798: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-799- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-996- -with-* | --with-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:997: ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-998- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1002- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1003: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1004- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1013- -without-* | --without-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1014: ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1015- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1019- ac_useropt_orig=$ac_useropt
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1020: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1021- case $ac_user_opts in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1053- *=*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1054: ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1055- # Reject names that are not valid shell variable names.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1073-if test -n "$ac_prev"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1074: ac_option=--`echo $ac_prev | sed 's/_/-/g'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1075- { $as_echo "$as_me: error: missing argument to $ac_option" >&2
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1097- */ )
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1098: ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1099- eval $ac_var=\$ac_val;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1135-ac_ls_di=`ls -di .` &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1136:ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1137- { $as_echo "$as_me: error: working directory cannot be determined" >&2
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1195-case $srcdir in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1196:*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1197-esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1238-By default, \`make install' will install all the files in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1239:\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1240:an installation prefix other than \`$ac_default_prefix' using \`--prefix',
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1241-for instance \`--prefix=\$HOME'.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1303-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1304: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1305- # A ".." for each directory in $ac_dir_suffix.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1306: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1307- case $ac_top_builddir_sub in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1436- *\'*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1437: ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1438- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1523- case $ac_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1524: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1525- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1540- case $ac_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1541: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1542- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1651- set,)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1652: { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1653:$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1654- ac_cache_corrupted=: ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1662- # differences in whitespace do not lead to failure.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1663: ac_old_val_w=`echo x $ac_old_val`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1664: ac_new_val_w=`echo x $ac_new_val`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1665- if test "$ac_old_val_w" != "$ac_new_val_w"; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1682- case $ac_new_val in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:1683: *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-1684- *) ac_arg=$ac_var=$ac_new_val ;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2099-$as_echo_n "checking for C compiler default output file name... " >&6; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2100:ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2101-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2143- then :; else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2144: ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2145- fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2246- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2247: *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2248- break;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2304- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2305: *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2306- break;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2860-'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2861:DEFS=`sed -n "$ac_script" confdefs.h`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2862-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2868- ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2869: ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2870- # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2938-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2939:if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2940- as_echo='printf %s\n'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2942-else
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2943: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2944- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2952- expr "X$arg" : "X\\(.*\\)$as_nl";
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:2953: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-2954- esac;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3068- test "x$as_lineno_1" != "x$as_lineno_2" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3069: test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3070-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3181- esac;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3182: case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3183- ???[sx]*):;;*)false;;esac;fi
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3253-configured by $0, generated by GNU Autoconf 2.63,
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3254: with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3255-
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3271- --*=*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3272: ac_option=`expr "X$1" : 'X\([^=]*\)='`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3273: ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3274- ac_shift=:
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3293- case $ac_optarg in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3294: *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3295- esac
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3407-ac_cr=''
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3408:ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3409-if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3426- { (exit 1); exit 1; }; }
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3427:ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3428-ac_delim='%!_!# '
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3434-
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3435: ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3436- if test $ac_delim_n = $ac_delim_num; then
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3596- esac
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3597: case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3598- ac_file_inputs="$ac_file_inputs '$ac_f'"
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3659- case $as_dir in #(
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3660: *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3661- *) as_qdir=$as_dir;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3697-*)
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3698: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3699- # A ".." for each directory in $ac_dir_suffix.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3700: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3701- case $ac_top_builddir_sub in
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3751-'
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3752:case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3753-*datarootdir*) ac_datarootdir_seen=yes;;
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3768-
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3769:# Neutralize VPATH when `$srcdir' = `.'.
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3770-# Shell code in configure.ac might set extrasub.
##############################################
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3796-test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3797: { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure:3798: { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
rsem-1.3.3+dfsg/pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/configure-3799- { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
##############################################
rsem-1.3.3+dfsg/rsem-calculate-expression-698- if ($alleleS) {
rsem-1.3.3+dfsg/rsem-calculate-expression:699: system("mv $sampleName.alleles.results $imdName.alleles.results.bak1");
rsem-1.3.3+dfsg/rsem-calculate-expression:700: system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak1");
rsem-1.3.3+dfsg/rsem-calculate-expression:701: system("mv $sampleName.genes.results $imdName.genes.results.bak1");
rsem-1.3.3+dfsg/rsem-calculate-expression-702- &collectResults("allele", "$imdName.allele_res", "$sampleName.alleles.results"); # allele level
##############################################
rsem-1.3.3+dfsg/rsem-calculate-expression-706- else {
rsem-1.3.3+dfsg/rsem-calculate-expression:707: system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak1");
rsem-1.3.3+dfsg/rsem-calculate-expression:708: system("mv $sampleName.genes.results $imdName.genes.results.bak1");
rsem-1.3.3+dfsg/rsem-calculate-expression-709- &collectResults("isoform", "$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
##############################################
rsem-1.3.3+dfsg/rsem-calculate-expression-722- if ($alleleS) {
rsem-1.3.3+dfsg/rsem-calculate-expression:723: system("mv $sampleName.alleles.results $imdName.alleles.results.bak2");
rsem-1.3.3+dfsg/rsem-calculate-expression:724: system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak2");
rsem-1.3.3+dfsg/rsem-calculate-expression:725: system("mv $sampleName.genes.results $imdName.genes.results.bak2");
rsem-1.3.3+dfsg/rsem-calculate-expression-726- &collectResults("allele", "$imdName.allele_res", "$sampleName.alleles.results"); # allele level
##############################################
rsem-1.3.3+dfsg/rsem-calculate-expression-730- else {
rsem-1.3.3+dfsg/rsem-calculate-expression:731: system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak2");
rsem-1.3.3+dfsg/rsem-calculate-expression:732: system("mv $sampleName.genes.results $imdName.genes.results.bak2");
rsem-1.3.3+dfsg/rsem-calculate-expression-733- &collectResults("isoform", "$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
##############################################
rsem-1.3.3+dfsg/rsem-calculate-expression-790-
rsem-1.3.3+dfsg/rsem-calculate-expression:791: system("head -8 $fiso_res > $fprsem_iso_res" );
rsem-1.3.3+dfsg/rsem-calculate-expression:792: system("tail -5 $fiso_res >> $fprsem_iso_res" );
rsem-1.3.3+dfsg/rsem-calculate-expression-793-
rsem-1.3.3+dfsg/rsem-calculate-expression:794: system("head -7 $fgene_res > $fprsem_gene_res");
rsem-1.3.3+dfsg/rsem-calculate-expression:795: system("tail -4 $fgene_res >> $fprsem_gene_res");
rsem-1.3.3+dfsg/rsem-calculate-expression-796-
##############################################
rsem-1.3.3+dfsg/rsem_perl_utils.pm-17- print $_[0]."\n";
rsem-1.3.3+dfsg/rsem_perl_utils.pm:18: my $status = system($_[0]);
rsem-1.3.3+dfsg/rsem_perl_utils.pm-19-
##############################################
rsem-1.3.3+dfsg/debian/tests/run-unit-test-8-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
rsem-1.3.3+dfsg/debian/tests/run-unit-test:9: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
rsem-1.3.3+dfsg/debian/tests/run-unit-test-10- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM