=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== bali-phy-3.5.0.2+dfsg/README.md-64- bali-phy-3.5.0.2+dfsg/README.md:65:Adding bali-phy to your `$PATH` bali-phy-3.5.0.2+dfsg/README.md-66------------------------------- ############################################## bali-phy-3.5.0.2+dfsg/README.md-72- bali-phy-3.5.0.2+dfsg/README.md:73:If you installed in `$HOME/Applications/bali-phy/` as recommended above, then files will be in: bali-phy-3.5.0.2+dfsg/README.md-74- ############################################## bali-phy-3.5.0.2+dfsg/haskell/Probability/Distribution/Categorical.hs-11-sample_categorical ps = RandomStructure (categorical_effect (length ps)) modifiable_structure $ liftIO (IOAction (\s->(s, raw_sample_categorical ps s))) bali-phy-3.5.0.2+dfsg/haskell/Probability/Distribution/Categorical.hs:12:-- FIXME: is `make_densities $ qs !` supposed to parse as `make_densities (qs!)`? bali-phy-3.5.0.2+dfsg/haskell/Probability/Distribution/Categorical.hs-13-categorical ps = Distribution (make_densities (qs!)) (no_quantile "categorical") (sample_categorical ps) (integer_between 0 (length ps - 1)) ############################################## bali-phy-3.5.0.2+dfsg/help/commands/package-path.txt-13- bali-phy-3.5.0.2+dfsg/help/commands/package-path.txt:14:where `$HOME` is the user's home directory, and `<exe>` is the directory bali-phy-3.5.0.2+dfsg/help/commands/package-path.txt-15-containing the `bali-phy` executable: ############################################## bali-phy-3.5.0.2+dfsg/scripts/bali-phy-pkg-589- my $data; bali-phy-3.5.0.2+dfsg/scripts/bali-phy-pkg:590: my $where = $fetcher->fetch( to => \$data ); bali-phy-3.5.0.2+dfsg/scripts/bali-phy-pkg-591- print "done.\n"; ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-1468- die "can't find script $script!" if (!defined($script)); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:1469: Rexec($script,"Results/LOD-table Results/convergence-PP.pdf"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-1470- } ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-1475- die "can't find script $script!" if (!defined($script)); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:1476: Rexec($script,"Results/LOD-table Results/convergence1-PP.svg Results/convergence2-PP.svg"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-1477- } ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3081- exec_show("trees-distances matrix --max=$N --jitter=0.3 $subsample_string $skip $tree_file > $matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3082: Rexec($script,"$matfile $outfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3083- ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3085- bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3086: my $point_string = Rexec($script3d, "$matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3087- &write_x3d_file("Results","tree-3D1-1.points", $point_string); ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3104- exec_show("trees-distances matrix --max=$N --jitter=0.3 $subsample_string $skip $tf1 $tf2 > $matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3105: Rexec($script,"$L1 $L2 $matfile $outfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3106- ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3108- # print "3d script is at '${script3d}'\n"; bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3109: my $point_string = Rexec($script3d, "$L1 $L2 $matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3110- ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3130- exec_show("trees-distances matrix --max=$N --jitter=0.3 $subsample_string $skip $tf1 $tf2 $tf3 > $matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3131: Rexec($script,"$L1 $L2 $L3 $matfile $outfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3132- ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3134- # print "3d script is at '${script3d}'\n"; bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3135: my $point_string = Rexec($script3d, "$L1 $L2 $L3 $matfile"); bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3136- ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3148- bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3149: my $result = `$cmd 2>$tmp_filename`; bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3150: my $message = `cat $tmp_filename`; bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3151- print $LOG $message; ############################################## bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3177- bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl:3178: my $result = `$cmd`; bali-phy-3.5.0.2+dfsg/scripts/bp-analyze.pl-3179- return $?; ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-66-# Who am I? bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:67:self=`basename "$0"` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-68- ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-89- else bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:90: ifndef_symbol=`basename "$outfile" | $SED 's|\.|_|g; s|[^A-Za-z0-9_]||g' | tr a-z A-Z` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-91- fi ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-138-# Done with creating output files, so we can change to source dir bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:139:abs_srcdir=`cd "$srcdir" && pwd` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-140-cd "$srcdir" ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-158-git_found=yes bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:159:if [ "x$GIT" = "xgit" ] && [ x`which $GIT 2>/dev/null` = "x" ]; then bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-160- git_found="'$GIT' not found" ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-167-if [ "x$git_found" = "xyes" ]; then bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:168: git_version=`$GIT --version` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-169- if [ "x$git_version" = "x" ]; then ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-183- # git-1.4 and probably earlier understand "git-rev-parse HEAD" bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:184: git_shaid=`$GIT rev-parse HEAD | $SED -n 's/^\(.\{8\}\).*/\1/p'` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-185- if [ "x$git_shaid" = "x" ]; then ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-189- # I also want the date! bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:190: # git_commit_date=`$GIT log -n 1 --pretty=format:%aD | date +"%b %d %Y %k:%M:%S"`; bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-191- bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-192- # git_commit_date=`date +"%b %d %Y %k:%M:%S" -d $($GIT log -n 1 --pretty=format:%aD) bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:193: git_commit_date=`$GIT log -n 1 --pretty=format:%aD`; bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-194- if date +"%b %d %Y %k:%M:%S" -d "$git_commit_date" >/dev/null 2>&1; then ############################################## bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-198- # git-1.4 and probably earlier understand "git-symbolic-ref HEAD" bali-phy-3.5.0.2+dfsg/scripts/git_version.sh:199: git_branch=`$GIT symbolic-ref HEAD | $SED -n 's|^refs/heads/||p'` bali-phy-3.5.0.2+dfsg/scripts/git_version.sh-200- if [ "x$git_branch" = "x" ]; then ############################################## bali-phy-3.5.0.2+dfsg/src/computation/machine/gc.cc-132- { bali-phy-3.5.0.2+dfsg/src/computation/machine/gc.cc:133: int r = i.addr(); bali-phy-3.5.0.2+dfsg/src/computation/machine/gc.cc-134- i++; ############################################## bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc-1445- { bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1446: int r1 = i.addr(); bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc-1447- ############################################## bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H-196- bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:197: int addr() const {return index;} bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H-198- ############################################## bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H-227- bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:228: int addr() const {return index;} bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H-229- ############################################## bali-phy-3.5.0.2+dfsg/src/computation/parser/parser.y-6-%define api.value.type variant bali-phy-3.5.0.2+dfsg/src/computation/parser/parser.y:7:// This could offer a speedup, but doesn't work with `if ($7) e.push_back($7)`. bali-phy-3.5.0.2+dfsg/src/computation/parser/parser.y-8-// %define api.value.automove ############################################## bali-phy-3.5.0.2+dfsg/debian/tests/run-unit-test-7-if [ "$AUTOPKGTEST_TMP" = "" ] ; then bali-phy-3.5.0.2+dfsg/debian/tests/run-unit-test:8: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` bali-phy-3.5.0.2+dfsg/debian/tests/run-unit-test-9- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM