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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-qtl-1.46-2/vignettes/bcsft.Rnw-179-
r-cran-qtl-1.46-2/vignettes/bcsft.Rnw:180:  where $w=1-r$.
r-cran-qtl-1.46-2/vignettes/bcsft.Rnw-181-
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r-cran-qtl-1.46-2/vignettes/bcsft.Rnw-330-
r-cran-qtl-1.46-2/vignettes/bcsft.Rnw:331:In the previous implementation of R/qtl recombination counts were calculated, however for advanced crossing schemes there is no direct analytic solution.  Instead we implemented a hill climbing algorithm using a golden section search \cite{Kiefer} which determines the most probable recombination frequency, rather than calculating an actual value.  The search space starts between 0 and 0.5 (all possible recombination frequencies).  The golden section search relies on comparing three points (figure \ref{search}).  To start with the points are $r=0$, $r=0.5$, and $r=r_1$, where the value of $r_1$ is determined so that the ratio of a to a+b is equal to the ratio of a to b.  Then a new point ($r=r_2$) is added in the larger interval so that the ratio of d to a is equal to the ratio of c to d.  The set of 3 $r$ values containing the highest maximum likelihood (as compared to the null model of unlinked markers $r=0.5$) are kept, and the remaining value is dropped (in this case $r=0.5$).  The search algorithm starts again with 0, $r_1$, and $r_2$ as the three points.  This process repeats until tolerance for the minimum improvement in likelihood is reached, then the $r$ value with the highest likelihood is reported as the maximum likelihodd estimate used in the map.  This provides an accurate estimate of recombination frequency.
r-cran-qtl-1.46-2/vignettes/bcsft.Rnw-332-
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r-cran-qtl-1.46-2/vignettes/vignette.bib-51-author = "S. D. Tanksley and J. C. Nelson",
r-cran-qtl-1.46-2/vignettes/vignette.bib:52:title = "Advanced backcross {QTL} analysis: a method for the simultaneous discovery and transfer of valuable {QTLs} from unadapted germplasm into elite breeding lines",
r-cran-qtl-1.46-2/vignettes/vignette.bib-53-year = "1996",
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r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw-179-
r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw:180:  where $w=1-r$.
r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw-181-
##############################################
r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw-330-
r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw:331:In the previous implementation of R/qtl recombination counts were calculated, however for advanced crossing schemes there is no direct analytic solution.  Instead we implemented a hill climbing algorithm using a golden section search \cite{Kiefer} which determines the most probable recombination frequency, rather than calculating an actual value.  The search space starts between 0 and 0.5 (all possible recombination frequencies).  The golden section search relies on comparing three points (figure \ref{search}).  To start with the points are $r=0$, $r=0.5$, and $r=r_1$, where the value of $r_1$ is determined so that the ratio of a to a+b is equal to the ratio of a to b.  Then a new point ($r=r_2$) is added in the larger interval so that the ratio of d to a is equal to the ratio of c to d.  The set of 3 $r$ values containing the highest maximum likelihood (as compared to the null model of unlinked markers $r=0.5$) are kept, and the remaining value is dropped (in this case $r=0.5$).  The search algorithm starts again with 0, $r_1$, and $r_2$ as the three points.  This process repeats until tolerance for the minimum improvement in likelihood is reached, then the $r$ value with the highest likelihood is reported as the maximum likelihodd estimate used in the map.  This provides an accurate estimate of recombination frequency.
r-cran-qtl-1.46-2/inst/doc/bcsft.Rnw-332-
##############################################
r-cran-qtl-1.46-2/inst/contrib/scripts/install_rqtl.sh-19-
r-cran-qtl-1.46-2/inst/contrib/scripts/install_rqtl.sh:20:rqtl_version=`grep Version DESCRIPTION | awk '{ print $2; }'`
r-cran-qtl-1.46-2/inst/contrib/scripts/install_rqtl.sh-21-
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r-cran-qtl-1.46-2/debian/tests/run-unit-test-4-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-cran-qtl-1.46-2/debian/tests/run-unit-test:5:  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
r-cran-qtl-1.46-2/debian/tests/run-unit-test-6-fi