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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-cran-cellranger-1.1.0/inst/doc/cell-references.Rmd-22- * as a string
r-cran-cellranger-1.1.0/inst/doc/cell-references.Rmd:23: - in A1 format: e.g. `B4`, `B$4`, `$B4`, `$B$4` (let's assume found in cell `D5`, shall we?)
r-cran-cellranger-1.1.0/inst/doc/cell-references.Rmd-24- - in R1C1 format: e.g. `R[1]C[-2]`, `R4C[-2]`, `R[1]C2`, `R4C2`
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-ra-ref-class.R-121-test_that("vectorized version of as.ra_ref.cell_addr works", {
r-cran-cellranger-1.1.0/tests/testthat/test-ra-ref-class.R:122: input <- cell_addr(1:3, 1)
r-cran-cellranger-1.1.0/tests/testthat/test-ra-ref-class.R-123- output <- list(ra_ref(), ra_ref(row_ref = 2), ra_ref(row_ref = 3))
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-3-test_that("cell_addr constructor requires row and col and checks lengths", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:4: expect_error(cell_addr(1))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:5: expect_error(cell_addr(1:2, 1:3))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-6-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-8-test_that("cell_addr constructor rejects row, column < 1", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:9: expect_error(cell_addr(1, -1))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:10: expect_error(cell_addr(-1, 1))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-11-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-13-test_that("cell_addr constructor works for single cell", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:14: ca <- cell_addr(3, 7)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-15- expect_is(ca, "cell_addr")
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-20-test_that("cell_addr constructor works for multiple cells", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:21: ca <- cell_addr(c(3, 10), c(7, 2))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-22- expect_is(ca, "cell_addr")
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-27-test_that("cell_addr constructor recycles length 1 row or col", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:28: ca <- cell_addr(1:3, 6)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-29- expect_is(ca, "cell_addr")
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-34-test_that("cell_addr constructor accepts NAs (and is not picky about type)", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:35: ca <- cell_addr(NA, NA)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-36- expect_is(ca, "cell_addr")
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-41-test_that("cell_addr `[` indexing works", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:42: ca <- cell_addr(1:3, 6)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:43: expect_identical(ca[c(1, 3)], cell_addr(c(1L, 3L), 6L))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:44: expect_identical(ca[-2], cell_addr(c(1L, 3L), 6L))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:45: expect_identical(ca[c(TRUE, FALSE, TRUE)], cell_addr(c(1L, 3L), 6L))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-46-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-48-test_that("cell_addr `[[` indexing works", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:49: ca <- cell_addr(1:3, 6)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:50: expect_identical(ca[[3]], cell_addr(3L, 6L))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-51- expect_error(ca[[-2]])
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-54-test_that("cell_addr length method works", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:55: ca <- cell_addr(1:3, 6)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-56- expect_length(ca, 3L)
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-59-test_that("row and column extraction work for cell_addr objects", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:60: ca <- cell_addr(1:3, 6)
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-61- expect_identical(addr_row(ca), 1:3)
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-65-test_that("cell_addr objects can be converted to ra_ref", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:66: expect_identical(as.ra_ref(cell_addr(2, 5)),
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-67- ra_ref(row_ref = 2, col_ref = 5))
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-70-test_that("cell_addr objects can be converted to string", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:71: expect_identical(to_string(cell_addr(3, 8)), "R3C8")
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:72: expect_identical(to_string(cell_addr(3, 8), fo = "A1"), "$H$3")
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:73: expect_identical(to_string(cell_addr(3, 8), fo = "A1", strict = FALSE), "H3")
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-74-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-76-test_that("valid ra_ref objects can be converted to cell_addr", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:77: expect_identical(as.cell_addr(ra_ref()), cell_addr(1, 1))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:78: expect_identical(as.cell_addr(ra_ref(2, TRUE, 5, TRUE)), cell_addr(2, 5))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-79-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-81-test_that("ra_ref objects w/ NAs become cell_addr objects with NAs", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:82: expect_warning(expect_identical(as.cell_addr(ra_ref(2, FALSE, 5, FALSE)),
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:83: cell_addr(NA, NA)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:84: expect_warning(expect_identical(as.cell_addr(ra_ref(2, TRUE, 5, FALSE)),
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:85: cell_addr(2, NA)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:86: expect_warning(expect_identical(as.cell_addr(ra_ref(2, FALSE, 5, TRUE)),
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:87: cell_addr(NA, 5)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-88-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-90-test_that("valid cell ref strings can be converted to cell_addr", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:91: expect_identical(as.cell_addr("$D$12"), cell_addr(12, 4))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:92: expect_identical(as.cell_addr("R4C3"), cell_addr(4, 3))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-93-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-95-test_that("relative refs in cell ref strings create NAs in cell_addr", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:96: expect_warning(expect_identical(as.cell_addr("$F2"), cell_addr(NA, 6)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:97: expect_warning(expect_identical(as.cell_addr("F$2"), cell_addr(2, NA)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:98: expect_warning(expect_identical(as.cell_addr("R4C[3]"), cell_addr(4, NA)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:99: expect_warning(expect_identical(as.cell_addr("RC"), cell_addr(NA, NA)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-100-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-102-test_that("relative cell ref strings convert to cell_addr if strict = FALSE", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:103: expect_identical(as.cell_addr("F2", strict = FALSE), as.cell_addr("$F$2"))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-104-})
##############################################
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-106-test_that("a vector of cell ref strings is converted to cell_addr", {
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:107: x <- as.cell_addr(c("$D$12", "$C$4"))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R:108: expect_identical(x, cell_addr(row = c(12L, 4L), col = c(4L, 3L)))
r-cran-cellranger-1.1.0/tests/testthat/test-cell-addr-class.R-109- y <- lapply(c("$D$12", "$C$4"), as.cell_addr)
##############################################
r-cran-cellranger-1.1.0/R/ra-ref.R-201-#' ## as.ra_ref.cell_addr
r-cran-cellranger-1.1.0/R/ra-ref.R:202:#' ca <- cell_addr(2, 5)
r-cran-cellranger-1.1.0/R/ra-ref.R-203-#' as.ra_ref(ca)
##############################################
r-cran-cellranger-1.1.0/R/ra-ref.R-212-#' @examples
r-cran-cellranger-1.1.0/R/ra-ref.R:213:#' ## as.ra_ref_v.cell_addr()
r-cran-cellranger-1.1.0/R/ra-ref.R-214-#'
r-cran-cellranger-1.1.0/R/ra-ref.R:215:#' ca <- cell_addr(1:3, 1)
r-cran-cellranger-1.1.0/R/ra-ref.R-216-#' \dontrun{
##############################################
r-cran-cellranger-1.1.0/R/to-string.R-102-#' ## cell_addr --> string
r-cran-cellranger-1.1.0/R/to-string.R:103:#' (ca <- cell_addr(3, 8))
r-cran-cellranger-1.1.0/R/to-string.R-104-#' to_string(ca)
##############################################
r-cran-cellranger-1.1.0/R/to-string.R-106-#'
r-cran-cellranger-1.1.0/R/to-string.R:107:#' (ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/R/to-string.R-108-#' to_string(ca)
##############################################
r-cran-cellranger-1.1.0/R/to-string.R-122-#' ## explicitly go from cell_addr, length > 1 --> character vector
r-cran-cellranger-1.1.0/R/to-string.R:123:#' (ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/R/to-string.R-124-#' to_string_v(ca)
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-19-#' @examples
r-cran-cellranger-1.1.0/R/cell-addr.R:20:#' cell_addr(4, 3)
r-cran-cellranger-1.1.0/R/cell-addr.R:21:#' (ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/R/cell-addr.R-22-#' ca[2:3]
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-58-`[.cell_addr` <-
r-cran-cellranger-1.1.0/R/cell-addr.R:59: function(x, i) cell_addr(row = addr_row(x)[i], col = addr_col(x)[i])
r-cran-cellranger-1.1.0/R/cell-addr.R-60-
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-62-`[[.cell_addr` <-
r-cran-cellranger-1.1.0/R/cell-addr.R:63: function(x, i) cell_addr(row = addr_row(x)[[i]], col = addr_col(x)[[i]])
r-cran-cellranger-1.1.0/R/cell-addr.R-64-
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-86-#' @describeIn addr_row Method for \code{\link{cell_addr}} objects
r-cran-cellranger-1.1.0/R/cell-addr.R:87:#' (ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/R/cell-addr.R-88-#' addr_row(ca)
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-92-#' @describeIn addr_col Method for \code{\link{cell_addr}} objects
r-cran-cellranger-1.1.0/R/cell-addr.R:93:#' (ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/R/cell-addr.R-94-#' addr_col(ca)
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-123-#' @examples
r-cran-cellranger-1.1.0/R/cell-addr.R:124:#' as.cell_addr(ra_ref())
r-cran-cellranger-1.1.0/R/cell-addr.R-125-#' rar <- ra_ref(2, TRUE, 5, TRUE)
r-cran-cellranger-1.1.0/R/cell-addr.R:126:#' as.cell_addr(rar)
r-cran-cellranger-1.1.0/R/cell-addr.R-127-#' ## mixed reference
r-cran-cellranger-1.1.0/R/cell-addr.R-128-#' rar <- ra_ref(2, FALSE, 5, TRUE)
r-cran-cellranger-1.1.0/R/cell-addr.R:129:#' as.cell_addr(rar)
r-cran-cellranger-1.1.0/R/cell-addr.R-130-as.cell_addr.ra_ref <- function(x, ...) {
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-139- }
r-cran-cellranger-1.1.0/R/cell-addr.R:140: cell_addr(row = x$row_ref, col = x$col_ref)
r-cran-cellranger-1.1.0/R/cell-addr.R-141-}
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-151- ca_list <- lapply(x, as.cell_addr)
r-cran-cellranger-1.1.0/R/cell-addr.R:152: cell_addr(row = vapply(ca_list, addr_row, integer(1)),
r-cran-cellranger-1.1.0/R/cell-addr.R-153- col = vapply(ca_list, addr_col, integer(1)))
##############################################
r-cran-cellranger-1.1.0/R/cell-addr.R-160-#' @examples
r-cran-cellranger-1.1.0/R/cell-addr.R:161:#' as.cell_addr("$D$12")
r-cran-cellranger-1.1.0/R/cell-addr.R:162:#' as.cell_addr("R4C3")
r-cran-cellranger-1.1.0/R/cell-addr.R:163:#' as.cell_addr(c("$C$4", "$D$12"))
r-cran-cellranger-1.1.0/R/cell-addr.R:164:#' as.cell_addr("$F2")
r-cran-cellranger-1.1.0/R/cell-addr.R:165:#' as.cell_addr("R[-4]C3")
r-cran-cellranger-1.1.0/R/cell-addr.R:166:#' as.cell_addr("F2", strict = FALSE)
r-cran-cellranger-1.1.0/R/cell-addr.R-167-as.cell_addr.character <- function(x, fo = NULL, strict = TRUE, ...) {
##############################################
r-cran-cellranger-1.1.0/R/cell-limits.R-169- if (anyNA(unlist(x[c("ul", "lr")]))) return(NA_character_)
r-cran-cellranger-1.1.0/R/cell-limits.R:170: ca <- cell_addr(c(x$ul[1], x$lr[1]), c(x$ul[2], x$lr[2]))
r-cran-cellranger-1.1.0/R/cell-limits.R-171- range <- paste(to_string(ca, fo = fo, strict = strict), collapse = ":")
##############################################
r-cran-cellranger-1.1.0/vignettes/cell-references.Rmd-22- * as a string
r-cran-cellranger-1.1.0/vignettes/cell-references.Rmd:23: - in A1 format: e.g. `B4`, `B$4`, `$B4`, `$B$4` (let's assume found in cell `D5`, shall we?)
r-cran-cellranger-1.1.0/vignettes/cell-references.Rmd-24- - in R1C1 format: e.g. `R[1]C[-2]`, `R4C[-2]`, `R[1]C2`, `R4C2`
##############################################
r-cran-cellranger-1.1.0/vignettes/cell-references.md-11- * as a string
r-cran-cellranger-1.1.0/vignettes/cell-references.md:12: - in A1 format: e.g. `B4`, `B$4`, `$B4`, `$B$4` (let's assume found in cell `D5`, shall we?)
r-cran-cellranger-1.1.0/vignettes/cell-references.md-13- - in R1C1 format: e.g. `R[1]C[-2]`, `R4C[-2]`, `R[1]C2`, `R4C2`
##############################################
r-cran-cellranger-1.1.0/man/addr_col.Rd-25-\item \code{cell_addr}: Method for \code{\link{cell_addr}} objects
r-cran-cellranger-1.1.0/man/addr_col.Rd:26:(ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/man/addr_col.Rd-27-addr_col(ca)
##############################################
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd-78-## as.ra_ref.cell_addr
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd:79:ca <- cell_addr(2, 5)
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd-80-as.ra_ref(ca)
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd:81:## as.ra_ref_v.cell_addr()
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd-82-
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd:83:ca <- cell_addr(1:3, 1)
r-cran-cellranger-1.1.0/man/as.ra_ref.Rd-84-\dontrun{
##############################################
r-cran-cellranger-1.1.0/man/cell_addr.Rd-6-\usage{
r-cran-cellranger-1.1.0/man/cell_addr.Rd:7:cell_addr(row, col)
r-cran-cellranger-1.1.0/man/cell_addr.Rd-8-}
##############################################
r-cran-cellranger-1.1.0/man/cell_addr.Rd-33-\examples{
r-cran-cellranger-1.1.0/man/cell_addr.Rd:34:cell_addr(4, 3)
r-cran-cellranger-1.1.0/man/cell_addr.Rd:35:(ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/man/cell_addr.Rd-36-ca[2:3]
##############################################
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-11-\usage{
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:12:as.cell_addr(x, ...)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-13-
##############################################
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-51-\examples{
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:52:as.cell_addr(ra_ref())
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-53-rar <- ra_ref(2, TRUE, 5, TRUE)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:54:as.cell_addr(rar)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-55-## mixed reference
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-56-rar <- ra_ref(2, FALSE, 5, TRUE)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:57:as.cell_addr(rar)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-58-ra_ref_list <-
##############################################
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-60-as.cell_addr_v(ra_ref_list)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:61:as.cell_addr("$D$12")
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:62:as.cell_addr("R4C3")
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:63:as.cell_addr(c("$C$4", "$D$12"))
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:64:as.cell_addr("$F2")
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:65:as.cell_addr("R[-4]C3")
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd:66:as.cell_addr("F2", strict = FALSE)
r-cran-cellranger-1.1.0/man/as.cell_addr.Rd-67-}
##############################################
r-cran-cellranger-1.1.0/man/addr_row.Rd-25-\item \code{cell_addr}: Method for \code{\link{cell_addr}} objects
r-cran-cellranger-1.1.0/man/addr_row.Rd:26:(ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/man/addr_row.Rd-27-addr_row(ca)
##############################################
r-cran-cellranger-1.1.0/man/to_string.Rd-87-## cell_addr --> string
r-cran-cellranger-1.1.0/man/to_string.Rd:88:(ca <- cell_addr(3, 8))
r-cran-cellranger-1.1.0/man/to_string.Rd-89-to_string(ca)
##############################################
r-cran-cellranger-1.1.0/man/to_string.Rd-91-
r-cran-cellranger-1.1.0/man/to_string.Rd:92:(ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/man/to_string.Rd-93-to_string(ca)
##############################################
r-cran-cellranger-1.1.0/man/to_string.Rd-95-## explicitly go from cell_addr, length > 1 --> character vector
r-cran-cellranger-1.1.0/man/to_string.Rd:96:(ca <- cell_addr(1:4, 3))
r-cran-cellranger-1.1.0/man/to_string.Rd-97-to_string_v(ca)