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/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R-34- nr.snps < nrow(snp.data)
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R:35: phenotype <- eval(m$phenotype, envir=data)
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R-36- if (is.factor(phenotype))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R-45- if (!smiss) {
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R:46: stratum <- as.integer(as.factor(eval(m$stratum, envir=data)))[which]
r-bioc-snpstats-1.40.0+dfsg/R/mvtests.R-47- sorder <- order(stratum)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-160- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:161: pedigree <- as.character(eval(mcall$pedigree, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-162- if (any(is.na(pedigree)))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-168- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:169: id <- as.character(eval(mcall$id, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-170- if (any(is.na(id)))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-176- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:177: father <- as.character(eval(mcall$father, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-178- father[is.na(father)] = as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-182- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:183: mother <- as.character(eval(mcall$mother, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-184- mother[is.na(mother)] = as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-188- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:189: sex <- as.numeric(eval(mcall$sex, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-190- sex[is.na(sex)] = as.numeric(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-195- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:196: phenotype <- as.numeric(eval(mcall$phenotype, envir=subject.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-197- phenotype[is.na(phenotype)] = as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-284- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:285: chromosome <- as.character(eval(mcall$chromosome, envir=snp.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-286- chromosome[is.na(chromosome)] <- as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-292- genetic.distance <-
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:293: as.numeric(eval(mcall$genetic.distance, envir=snp.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-294- genetic.distance[is.na(genetic.distance)] <- as.numeric(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-299- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:300: position <- as.numeric(eval(mcall$position, envir=snp.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-301- position[is.na(position)] <- as.numeric(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-306- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:307: allele.1 <- as.character(eval(mcall$allele.1, envir=snp.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-308- allele.1[is.na(allele.1)] <- as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-313- else {
r-bioc-snpstats-1.40.0+dfsg/R/plink.R:314: allele.2 <- as.character(eval(mcall$allele.2, envir=snp.data))[sord]
r-bioc-snpstats-1.40.0+dfsg/R/plink.R-315- allele.2[is.na(allele.2)] <- as.character(na.code)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/single.R-49- which <- match(nm.snps, nm.data, nomatch=NA)
r-bioc-snpstats-1.40.0+dfsg/R/single.R:50: phenotype <- as.numeric(eval(m$phenotype, envir=data))[which]
r-bioc-snpstats-1.40.0+dfsg/R/single.R-51- complt <- !is.na(phenotype)
r-bioc-snpstats-1.40.0+dfsg/R/single.R-52- if (!smiss) {
r-bioc-snpstats-1.40.0+dfsg/R/single.R:53: stratum <- as.integer(as.factor(eval(m$stratum, envir=data)))[which]
r-bioc-snpstats-1.40.0+dfsg/R/single.R-54- complt <- complt & !is.na(stratum)
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/single.R-56- if (!ssmiss) {
r-bioc-snpstats-1.40.0+dfsg/R/single.R:57: subset <- eval(m$subset, envir=data)
r-bioc-snpstats-1.40.0+dfsg/R/single.R-58- if (is.logical(subset)) {
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-46- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:47: ped <- as.character(eval(mcall$ped, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-48- if (is.null(ped))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-53- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:54: id <- as.character(eval(mcall$id, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-55- if(is.null(id))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-60- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:61: father <- as.character(eval(mcall$father, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-62- if(is.null(father))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-67- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:68: mother <- as.character(eval(mcall$mother, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-69- if(is.null(mother))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-74- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:75: affected <- as.logical(eval(mcall$affected, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-76- if(is.null(affected))
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-186- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:187: ped <- as.character(eval(mcall$ped, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-188-
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-191- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:192: id <- as.character(eval(mcall$id, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-193-
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-196- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:197: father <- as.character(eval(mcall$father, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-198-
##############################################
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-201- else
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R:202: mother <- as.character(eval(mcall$mother, envir=data))
r-bioc-snpstats-1.40.0+dfsg/R/tdt-single.R-203-
##############################################
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-3-biocname=snpStats
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test:4:pkg=r-bioc-`echo $biocname | tr '[A-Z]' '[a-z]'`
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-5-
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-8-fi
##############################################
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-14- echo "====================== $rnw ============================"
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test:15: rfile=`basename $rnw nw`
r-bioc-snpstats-1.40.0+dfsg/debian/tests/run-unit-test-16- if [ "$rnw" = "imputation-vignette.Rnw" ] ; then # -o "$rnw" = "ld-vignette.Rnw" ]