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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-openmx-2.18.1/demo/UnivariateTwinAnalysis_MatrixRaw.R-121-estMean <- mxEval(mean, twinACEFit) # expected mean
r-cran-openmx-2.18.1/demo/UnivariateTwinAnalysis_MatrixRaw.R:122:estCovMZ <- mxEval(expCovMZ, twinACEFit$MZ) # expected covariance matrix for MZ's
r-cran-openmx-2.18.1/demo/UnivariateTwinAnalysis_MatrixRaw.R:123:estCovDZ <- mxEval(expCovDZ, twinACEFit$DZ) # expected covariance matrix for DZ's
r-cran-openmx-2.18.1/demo/UnivariateTwinAnalysis_MatrixRaw.R-124-estVA <- mxEval(a*a, twinACEFit) # additive genetic variance, a^2
##############################################
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R-360-omxCheckCloseEnough(modelOut[['test11b']]$result, t(-A$values), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:361:omxCheckCloseEnough(mxEval(test12, modelOut), cbind(A$values, B$values), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:362:omxCheckCloseEnough(mxEval(test12a, modelOut), cbind(t(A$values), B$values), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:363:omxCheckCloseEnough(mxEval(test12b, modelOut), cbind(A$values, t(B$values)), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:364:omxCheckCloseEnough(mxEval(test13, modelOut), rbind(A$values, B$values), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:365:omxCheckCloseEnough(mxEval(test13a, modelOut), rbind(t(A$values), B$values), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R:366:omxCheckCloseEnough(mxEval(test13b, modelOut), rbind(A$values, t(B$values)), 0.001)
r-cran-openmx-2.18.1/tests/testthat/test-AlgebraComputePassing.R-367-omxCheckCloseEnough(modelOut[['test14']]$result, det(A$values), 0.001)
##############################################
r-cran-openmx-2.18.1/src/omxState.cpp-700- SETCADR(theCall, Rmsg);
r-cran-openmx-2.18.1/src/omxState.cpp:701: SETCADDR(theCall, Rf_ScalarInteger(previousReport.length())); // not UTF8 safe TODO
r-cran-openmx-2.18.1/src/omxState.cpp-702- Rf_eval(theCall, R_GlobalEnv);
##############################################
r-cran-openmx-2.18.1/src/Compute.cpp-1021- SETCADR(theCall, rFitFunction->model);
r-cran-openmx-2.18.1/src/Compute.cpp:1022: SETCADDR(theCall, rFitFunction->flatModel);
r-cran-openmx-2.18.1/src/Compute.cpp-1023- SETCADDDR(theCall, estimate);
##############################################
r-cran-openmx-2.18.1/src/omxRFitFunction.cpp-32- SETCADR(theCall, rFitFunction->model);
r-cran-openmx-2.18.1/src/omxRFitFunction.cpp:33: SETCADDR(theCall, rFitFunction->state);
r-cran-openmx-2.18.1/src/omxRFitFunction.cpp-34-
##############################################
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-34-SVN_ROOT=$1
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh:35:OUTPUT_DIR=`cd $2; pwd`
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-36-START_REVISION=$3
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-37-END_REVISION=$4
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh:38:OPENMX_DIR=`cd $5; pwd`
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-39-
##############################################
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-52- set $line
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh:53: location=`basename $1`
r-cran-openmx-2.18.1/inst/tools/regressionTesting.sh-54- echo -e "$rev\t$2" >> $OUTPUT_DIR/$location.results
##############################################
r-cran-openmx-2.18.1/inst/tools/install-sh-211- fi
r-cran-openmx-2.18.1/inst/tools/install-sh:212: cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
r-cran-openmx-2.18.1/inst/tools/install-sh-213- *)
##############################################
r-cran-openmx-2.18.1/inst/tools/install-sh-263- dstdir=$dst
r-cran-openmx-2.18.1/inst/tools/install-sh:264: dst=$dstdir/`basename "$src"`
r-cran-openmx-2.18.1/inst/tools/install-sh-265- dstdir_status=0
##############################################
r-cran-openmx-2.18.1/inst/tools/install-sh-345- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
r-cran-openmx-2.18.1/inst/tools/install-sh:346: ls_ld_tmpdir=`ls -ld "$tmpdir"`
r-cran-openmx-2.18.1/inst/tools/install-sh-347- case $ls_ld_tmpdir in
##############################################
r-cran-openmx-2.18.1/inst/tools/install-sh-352- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
r-cran-openmx-2.18.1/inst/tools/install-sh:353: ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
r-cran-openmx-2.18.1/inst/tools/install-sh-354- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
##############################################
r-cran-openmx-2.18.1/inst/tools/install-sh-419- case $prefix in
r-cran-openmx-2.18.1/inst/tools/install-sh:420: *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
r-cran-openmx-2.18.1/inst/tools/install-sh-421- *) qprefix=$prefix;;
##############################################
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitions.R-222-omxCheckCloseEnough(rsgcmmDiffTFit$output$Minus2LogLikelihood, 9933, 170)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitions.R:223:#omxCheckCloseEnough(max(mxEval(rsgcmmFit$output$transitionProbs, rsgcmmFit)), 0.4790, 0.01)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitions.R:224:#omxCheckCloseEnough(min(mxEval(rsgcmmFit$output$transitionProbs, rsgcmmFit)), 0.1608, 0.01)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitions.R-225-## -----------------------------------------------------------------------------
##############################################
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R-216-omxCheckCloseEnough(rsgcmmDiffTFit$output$Minus2LogLikelihood, 11346.54, 0.01)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R:217:#omxCheckCloseEnough(max(mxEval(rsgcmmFit$output$transitionProbs, rsgcmmFit)), 0.4790, 0.01)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R:218:#omxCheckCloseEnough(min(mxEval(rsgcmmFit$output$transitionProbs, rsgcmmFit)), 0.1608, 0.01)
r-cran-openmx-2.18.1/inst/models/nightly/RegimeSwitching_MatrixRawNoCholDifferentTransitionsAllFixed.R-219-## -----------------------------------------------------------------------------
##############################################
r-cran-openmx-2.18.1/inst/models/passing/StateSpaceAlg.R-139-
r-cran-openmx-2.18.1/inst/models/passing/StateSpaceAlg.R:140:omxCheckCloseEnough(attr(mxEval(StateSpaceExample.fitfunction, srunS), "likelihoods"), attr(srunS$StateSpaceExample.fitfunction$result, "likelihoods"), epsilon=1e-8)
r-cran-openmx-2.18.1/inst/models/passing/StateSpaceAlg.R-141-
##############################################
r-cran-openmx-2.18.1/inst/models/passing/SummaryCheck.R-109-
r-cran-openmx-2.18.1/inst/models/passing/SummaryCheck.R:110:omxCheckEquals(dim(mxEval(satCov, mg.sat[[1]]$`Saturated OneFactor`))[1], 5)
r-cran-openmx-2.18.1/inst/models/passing/SummaryCheck.R:111:omxCheckEquals(dim(mxEval(satCov, mg.sat[[1]]$`Saturated OneVarFewer`))[1], 4)
r-cran-openmx-2.18.1/inst/models/passing/SummaryCheck.R-112-# the saturated model for OneVarFewer should be only on the variables used x2:x5, not all the variables x1:x5.
##############################################
r-cran-openmx-2.18.1/inst/models/passing/SaturatedWLSTest.R-130-
r-cran-openmx-2.18.1/inst/models/passing/SaturatedWLSTest.R:131:omxCheckCloseEnough(mxEval(satCov, model=satwls2Run), obsStats$cov, 1e-4)
r-cran-openmx-2.18.1/inst/models/passing/SaturatedWLSTest.R:132:omxCheckCloseEnough(mxEval(thresholdMatrix, model=satwls2Run)[-2], obsStats$thresholds[-2], 1e-2)
r-cran-openmx-2.18.1/inst/models/passing/SaturatedWLSTest.R-133-omxCheckCloseEnough(mxEval(fitfunction, model=satwls2Run), 0, 1e-3)
##############################################
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-59-
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R:60:omxCheckCloseEnough(testrun2$output$fit+mxEval(X[1,1] - X[2,1] - X[3,1] + 1, testrun2, T), testrun1$output$fit, 1e-7)
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-61-
##############################################
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-86-
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R:87:omxCheckCloseEnough(testrun3$output$fit+mxEval(X[1,1] - X[2,1] - X[3,1] + 1, testrun3, T), testrun1$output$fit, 1e-7)
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-88-
##############################################
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-108-summary(testrun4)
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R:109:omxCheckCloseEnough(testrun4$output$fit+mxEval(X[1,1] - X[2,1] - X[3,1] + 1, testrun4, T), testrun1$output$fit, 1e-7)
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-110-#PseudoHessian shouldn't be calculated when using l1p:
##############################################
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R-132-summary(testrun5)
r-cran-openmx-2.18.1/inst/models/passing/NelderMeadTest--ineqConstraints.R:133:omxCheckCloseEnough(testrun5$output$fit+mxEval(X[1,1] - X[2,1] - X[3,1] + 1, testrun5, T), testrun1$output$fit, 1e-7)
##############################################
r-cran-openmx-2.18.1/configure-54-
r-cran-openmx-2.18.1/configure:55:CXX=`$REXEC CMD config CXX`
r-cran-openmx-2.18.1/configure-56-
##############################################
r-cran-openmx-2.18.1/configure-68-if [ "$cxx_type" = gcc ]; then
r-cran-openmx-2.18.1/configure:69: cxx_version=`$CXX -dumpfullversion -dumpversion | awk -F '.' '{print $1 "." $2}'`
r-cran-openmx-2.18.1/configure-70- #echo "gcc -> $cxx_version"
##############################################
r-cran-openmx-2.18.1/configure-122- pick="linux/${omx_arch}/gcc${cxx_version}"
r-cran-openmx-2.18.1/configure:123: want=`grep "$pick" inst/npsol/checksum | cut -f1 -d' ' | head -1`
r-cran-openmx-2.18.1/configure-124- npsol_url1="http://$wwwHome/packages/npsol/linux/${omx_arch}/$want"
##############################################
r-cran-openmx-2.18.1/configure-174-
r-cran-openmx-2.18.1/configure:175:# if [ `$REXEC --slave --vanilla -e 'cat(suppressWarnings(require("nloptr", quietly=TRUE)) && packageVersion("nloptr") >= "1.0.5")'` = TRUE ]; then
r-cran-openmx-2.18.1/configure-176-# echo "
r-cran-openmx-2.18.1/configure:177:# NLOPT_CXXFLAGS=`$REXEC --slave --vanilla -e 'suppressPackageStartupMessages(require(nloptr)); cat("-DHAS_NLOPT", nloptr:::CFlags())'`
r-cran-openmx-2.18.1/configure:178:# NLOPT_LDFLAGS=`$REXEC --slave --vanilla -e 'suppressPackageStartupMessages(require(nloptr)); cat(nloptr:::LdFlags())'`
r-cran-openmx-2.18.1/configure-179-# " >> src/Makevars.new
##############################################
r-cran-openmx-2.18.1/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-cran-openmx-2.18.1/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${debname}-test.XXXXXX`
r-cran-openmx-2.18.1/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM