===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beast-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/beauti-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/loganalyser-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/logcombiner-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treeannotator-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-13- else
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat:20: BEAST0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat:21: BEAST=`cd "$BEAST0" && pwd`
beast-mcmc-1.10.4+dfsg/release/Linux/scripts/treestat-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-13- else
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen:20: BEASTGEN0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen:21: BEASTGEN=`cd "$BEASTGEN0" && pwd`
beast-mcmc-1.10.4+dfsg/release_beastgen/common/bin/beastgen-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen:20: BEASTGEN0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen:21: BEASTGEN=`cd "$BEASTGEN0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/beastgen-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml:20: PHYLOGEOGRAPHY0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml:21: PHYLOGEOGRAPHY=`cd "$PHYLOGEOGRAPHY0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/continuous_tree_to_kml-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator:20: PHYLOGEOGRAPHY0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator:21: PHYLOGEOGRAPHY=`cd "$PHYLOGEOGRAPHY0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_rate_prior_generator-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml:20: PHYLOGEOGRAPHY0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml:21: PHYLOGEOGRAPHY=`cd "$PHYLOGEOGRAPHY0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/discrete_tree_to_kml-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf:20: PHYLOGEOGRAPHY0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf:21: PHYLOGEOGRAPHY=`cd "$PHYLOGEOGRAPHY0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/rate_indicator_bf-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-13- else
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer:20: PHYLOGEOGRAPHY0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer:21: PHYLOGEOGRAPHY=`cd "$PHYLOGEOGRAPHY0" && pwd`
beast-mcmc-1.10.4+dfsg/release_phylogeography/common/bin/timeslicer-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-8- while [ -h "$PRG" ] ; do
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss:9: ls=`ls -ld "$PRG"`
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss:10: link=`expr "$ls" : '.*-> \(.*\)$'`
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-11- if expr "$link" : '/.*' > /dev/null; then
##############################################
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-13- else
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss:14: PRG="`dirname "$PRG"`/$link"
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-15- fi
##############################################
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-19- saveddir=`pwd`
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss:20: PIBUSS0=`dirname "$PRG"`/..
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss:21: PIBUSS=`cd "$PIBUSS0" && pwd`
beast-mcmc-1.10.4+dfsg/release_pibuss/Linux/scripts/pibuss-22- cd "$saveddir"
##############################################
beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/TreeClusteringVirusesPrior.java-495- //Saturated prior: allows each $\pi_j$ to be different. $\pi_j$ is assumed to follow the hierarchical $Beta(\alpha, \beta)$ distribution, where $\alpha$ and $\beta$ are fixed according to plausible prior belief. The $Beta$ distribution is chosen because it is conjugate to the categorical distribution, so Gibbs sampling can be accomplished for $\pi$ (See details in the Implementation).
beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/TreeClusteringVirusesPrior.java:496: //Shrinkage Prior: models the belief about epitope and non-epitope sites. Here, we define a latent vector of binary indicators for amino acid positions $\delta = (\delta_1, \dots, \delta_L)$, where $\delta_k= 1$ if position $j$ is an epitope site and 0 otherwise.
beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/TreeClusteringVirusesPrior.java-497- //correlated prior: models the correlation among amino acid positions being epitopes or not (Figure \ref{correlationPrior}). This prior is motivated by the knowledge that groups of epitope sites tend to occur at adjacent positions.
##############################################
beast-mcmc-1.10.4+dfsg/debian/tests/run-unit-test-3-if [ "$ADTTMP" = "" ] ; then
beast-mcmc-1.10.4+dfsg/debian/tests/run-unit-test:4: ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
beast-mcmc-1.10.4+dfsg/debian/tests/run-unit-test-5-fi