[BZ-18658] Fixes to examples running with only base attached

src/library/base/man/Quotes.Rd

@@ -148,7 +148,7 @@ writeLines(x) # see also ?strwrap
 ## non-standard.)
 `x y` <- 1:5
 `x y`
-d <- data.frame(`1st column` = rchisq(5, 2), check.names = FALSE)
+d <- data.frame(`1st column` = stats::rchisq(5, 2), check.names = FALSE)
 d$`1st column`
 
 ## Backslashes followed by up to three numbers are interpreted as

src/library/base/man/Sys.getenv.Rd

@@ -59,7 +59,7 @@ Sys.getenv(c("R_HOME", "R_PAPERSIZE", "R_PRINTCMD", "HOST"))
 s <- Sys.getenv() # *all* environment variables
 op <- options(width=111) # (nice printing)
 names(s)    # all settings (the values could be very long)
-head(s, 12) # using the Dlist print() method
+utils::head(s, 12) # using the Dlist print() method
 
 ## Language and Locale settings -- but rather use Sys.getlocale()
 s[grep("^L(C|ANG)", names(s))]

src/library/base/man/Trig.Rd

@@ -116,7 +116,7 @@ x <- seq(-3, 7, by = 1/8)
 tx <- cbind(x, cos(pi*x), cospi(x), sin(pi*x), sinpi(x),
                tan(pi*x), tanpi(x), deparse.level=2)
 op <- options(digits = 4, width = 90) # for nice formatting
-head(tx)
+utils::head(tx)
 tx[ (x \%\% 1) \%in\% c(0, 0.5) ,]
 options(op)
 }

src/library/base/man/as.POSIXlt.Rd

@@ -169,7 +169,7 @@ as.POSIXct(strptime("2010-10-31 01:30:00", "\%Y-\%m-\%d \%H:\%M:\%S"))
 unclass(z)                    # a large integer
 floor(unclass(z)/86400)       # the number of days since 1970-01-01 (UTC)
 (now <- as.POSIXlt(Sys.time())) # the current datetime, as class "POSIXlt"
-str(unclass(now))             # the internal list ; use now$hour, etc :
+utils::str(unclass(now))      # the internal list ; use now$hour, etc :
 now$year + 1900               # see ?DateTimeClasses
 months(now); weekdays(now)    # see ?months; using LC_TIME locale
 

src/library/base/man/balancePOSIXlt.Rd

@@ -76,14 +76,14 @@ Sys.setenv(TZ = "UTC")
 d1 <- as.POSIXlt("2000-01-02 3:45")
 d1$min <- d1$min + (0:16)*20L
 (f1 <- format(d1))
-str(unclass(d1))      # only $min is of length > 1
+utils::str(unclass(d1))      # only $min is of length > 1
 df <- balancePOSIXlt(d1, fill.only = TRUE) # a "POSIXlt" object
-str(unclass(df))      # all of length 17; 'min' unchanged
+utils::str(unclass(df))      # all of length 17; 'min' unchanged
 db <- balancePOSIXlt(d1, classed = FALSE)  # a list
 stopifnot(identical(
     unCfillPOSIXlt(d1),
     balancePOSIXlt(d1, fill.only = TRUE, classed = FALSE)))
-str(db) # of length 17 *and* in range
+utils::str(db) # of length 17 *and* in range
 \dontshow{
 stopifnot(exprs = {
     identical(f1, format(df))

src/library/base/man/call.Rd

@@ -121,8 +121,10 @@ g
 eval(g)
 
 ## Special calls (and some regular ones):
-L <- as.list(E <- setNames( , c("if", "for", "while", "repeat", "function",
-                                  "(", "{", "[",  "<-", "<<-", "->", "=")))
+E <- c("if", "for", "while", "repeat", "function",
+       "(", "{", "[",  "<-", "<<-", "->", "=")
+names(E) <- E
+L <- as.list(E)
 for(i in seq_along(L)) L[[i]] <- call(E[[i]]) # instead of lapply(E, call) ..
 list_ <- function (...) `names<-`(list(...), vapply(sys.call()[-1L], as.character, ""))
 (Tab <- noquote(sapply(list_(is.call, typeof, class, mode), \(F) sapply(L, F))))

src/library/base/man/cbind.Rd

@@ -198,8 +198,8 @@ rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rownames (default)
 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 2) # 4 rownames
 
 ## cheap row names:
-b0 <- gl(3,4, labels=letters[1:3])
-bf <- setNames(b0, paste0("o", seq_along(b0)))
+b0 <- bf <- gl(3,4, labels=letters[1:3])
+names(bf) <- paste0("o", seq_along(b0))
 df  <- data.frame(a = 1, B = b0, f = gl(4,3))
 df. <- data.frame(a = 1, B = bf, f = gl(4,3))
 new <- data.frame(a = 8, B ="B", f = "1")

src/library/base/man/chkDots.Rd

@@ -29,6 +29,7 @@ seq.default ## <- you will see  ' chkDots(...) '
 seq(1,5, foo = "bar") # gives warning via chkDots()
 
 ## warning with more than one ...-entry:
+require(stats)
 density.f <- function(x, ...) NextMethod("density")
 x <- density(structure(rnorm(10), class="f"), bar=TRUE, baz=TRUE)
 }

src/library/base/man/cut.POSIXt.Rd

@@ -71,9 +71,9 @@ cut(as.Date("2001/1/1") + 70*stats::runif(100), "weeks")
 # The standards all have midnight as the start of the day, but some
 # people incorrectly interpret it at the end of the previous day ...
 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", length.out = 24)
-aggregate(1:24, list(day = cut(tm, "days")), mean)
+stats::aggregate(1:24, list(day = cut(tm, "days")), mean)
 # and a version with midnight included in the previous day:
-aggregate(1:24, list(day = cut(tm, "days", right = TRUE)), mean)
+stats::aggregate(1:24, list(day = cut(tm, "days", right = TRUE)), mean)
 }
 \keyword{manip}
 \keyword{chron}

src/library/base/man/dimnames.Rd

@@ -106,8 +106,8 @@ colnames0 <- function(x) dimnames(x)[[2]]
 A0 <- A; dimnames(A)[2:3] <- list(NULL)
 stopifnot(identical(A0, provideDimnames(A)))
 strd <- function(x) utils::str(dimnames(x))
-strd(provideDimnames(A, base= list(letters[-(1:9)], tail(LETTERS))))
-strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTERS)))) # recycling
+strd(provideDimnames(A, base= list(letters[-(1:9)], utils::tail(LETTERS))))
+strd(provideDimnames(N, base= list(letters[-(1:9)], utils::tail(LETTERS)))) # recycling
 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels
 ## set "empty dimnames":
 provideDimnames(rbind(1, 2:3), base = list(""), unique=FALSE)

src/library/base/man/dput.Rd

@@ -103,7 +103,7 @@ dget(fil) - xx # slight rounding on some platforms
 dput(xx, fil, control = "hexNumeric"); dget(fil) - xx
 unlink(fil)
 
-xn <- setNames(xx, paste0("pi^",1:3))
+xn <- stats::setNames(xx, paste0("pi^",1:3))
 dput(xn) # nicer, now "niceNames" being part of default 'control'
 dput(xn, control = "S_compat") # no names
 ## explicitly asking for output as in R < 3.5.0:

src/library/base/man/formals.Rd

@@ -64,7 +64,7 @@ names(formals(lm))
 methods:: formalArgs(lm)     # same
 
 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).
-str(formals(lm))
+utils::str(formals(lm))
 
 ## formals returns NULL for primitive functions.  Use it in combination with
 ## args for this case.

src/library/base/man/format.Rd

@@ -182,7 +182,7 @@ format(2^31-1)
 format(2^31-1, scientific = TRUE)
 ## scientific = numeric scipen (= {sci}entific notation {pen}alty) :
 x <- c(1e5, 1000, 10, 0.1, .001, .123)
-t(sapply(setNames(,-4:1),
+t(sapply(stats::setNames(,-4:1),
          \(sci) sapply(x, format, scientific=sci)))
 
 

src/library/base/man/formatc.Rd

@@ -297,7 +297,7 @@ stopifnot(pnv == "1+1i", pnv == format(zv),
           pnv == prettyNum(zv, drop0trailing = TRUE))
 ## more digits change the picture:
 options(digits = 8)
-head(fv <- format(zv), 3)
+utils::head(fv <- format(zv), 3)
 prettyNum(fv)
 prettyNum(fv, drop0trailing = TRUE) # a bit nicer
 options(op)

src/library/base/man/gzcon.Rd

@@ -55,7 +55,7 @@ z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch12.dat.gz"))
 # read.table can only read from a text-mode connection.
 raw <- textConnection(readLines(z))
 close(z)
-dat <- read.table(raw)
+dat <- utils::read.table(raw)
 close(raw)
 dat[1:4, ]
 }

src/library/base/man/iconv.Rd

@@ -232,7 +232,7 @@ try(iconv(x, "latin1", "ASCII//TRANSLIT"))  # platform-dependent
 iconv(x, "latin1", "ASCII", sub = "byte")
 
 ## and for Windows' 'Unicode'
-str(xx <- iconv(x, "latin1", "UTF-16LE", toRaw = TRUE))
+utils::str(xx <- iconv(x, "latin1", "UTF-16LE", toRaw = TRUE))
 iconv(xx, "UTF-16LE", "UTF-8")
 
 emoji <- "\U0001f604"

src/library/base/man/identical.Rd

@@ -157,7 +157,7 @@ identical(f, g)                        # TRUE, as bytecode is ignored by default
 identical(f, g, ignore.bytecode=FALSE) # FALSE: bytecode differs
 
 ## GLM families contain several functions, some of which share an environment:
-p1 <- poisson() ; p2 <- poisson()
+p1 <- stats::poisson() ; p2 <- stats::poisson()
 identical(p1, p2)                          # FALSE
 identical(p1, p2, ignore.environment=TRUE) # TRUE
 

src/library/base/man/ifelse.Rd

@@ -80,7 +80,7 @@ ifelse(x >= 0, sqrt(x), NA)
 x <- seq(as.Date("2000-02-29"), as.Date("2004-10-04"), by = "1 month")
 ## has many "yyyy-mm-29", but a few "yyyy-03-01" in the non-leap years
 y <- ifelse(as.POSIXlt(x)$mday == 29, x, NA)
-head(y) # not what you expected ... ==> need restore the class attribute:
+utils::head(y) # not what you expected ... ==> need restore the class attribute:
 class(y) <- class(x)
 y
 ## This is a (not atypical) case where it is better *not* to use ifelse(),

src/library/base/man/library.dynam.Rd

@@ -118,6 +118,7 @@ library.dynam()
 
 ## More on library.dynam.unload() :
 \donttest{require(nlme)
+require(utils)
 nlme:::.onUnload # shows library.dynam.unload() call
 detach("package:nlme")  # by default, unload=FALSE ,  so,
 tail(library.dynam(), 2)# nlme still there

src/library/base/man/list2env.Rd

@@ -63,7 +63,8 @@ stopifnot(identical(L [sort.list(names(L ))],
 
 ## now add to e -- can be seen as a fast "multi-assign":
 list2env(list(abc = LETTERS, note = "just an example",
-              df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),
+              df = data.frame(x = stats::rnorm(20),
+                              y = stats::rbinom(20, 1, prob = 0.2))),
          envir = e)
 utils::ls.str(e)
 }

src/library/base/man/locales.Rd

@@ -197,7 +197,7 @@ Sys.setenv("LANGUAGE" = "es") # set the language for error/warning messages
  ##' show a "full" Sys.getlocale() nicely:
  showL <- function(loc) {
      sl <- strsplit(strsplit(loc, sep)[[1L]], "=")
-     setNames(sapply(sl, `[[`, 2L), sapply(sl, `[[`, 1L))
+     stats::setNames(sapply(sl, `[[`, 2L), sapply(sl, `[[`, 1L))
  }
  print.Dlist(lloc <- showL(Sys.getlocale()))
  ## R-supported ones (but LC_ALL):

src/library/base/man/match.Rd

@@ -126,8 +126,8 @@ unique(zN) # the "NA" and the 3 different non-NA NaN's
 stopifnot(identical(unique(zN), zN[c(1, 7,9,10)]))
 
 ## very strict equality would have 4 duplicates (of 12):
-symnum(outer(zN, zN, Vectorize(identical,c("x","y")),
-                     FALSE,FALSE,FALSE,FALSE))
+stats::symnum(outer(zN, zN, Vectorize(identical,c("x","y")),
+                            FALSE,FALSE,FALSE,FALSE))
 ## removing "(very strictly) duplicates",
 i <- c(5,8,11,12)  # we get 8 pairwise non-identicals :
 Ixy <- outer(zN[-i], zN[-i], Vectorize(identical,c("x","y")),

src/library/base/man/nchar.Rd

@@ -153,7 +153,7 @@ nchar(deparse(mean))
 # 18 17  <-- unless mean differs from base::mean
 
 ## NA behaviour as function of keepNA=* :
-logi <- setNames(, c(FALSE, NA, TRUE))
+logi <- stats::setNames(, c(FALSE, NA, TRUE))
 sapply(logi, \(k) data.frame(nchar =  nchar (NA, keepNA=k),
                              nzchar = nzchar(NA, keepNA=k)))
 

src/library/base/man/parse.Rd

@@ -192,7 +192,7 @@ an error
 "
 sf <- srcfile("txt")
 tryCatch(parse(text = txt, srcfile = sf), error = function(e) "Syntax error.")
-getParseData(sf)
+utils::getParseData(sf)
 }
 \keyword{file}
 \keyword{programming}

src/library/base/man/pipeOp.Rd

@@ -59,8 +59,9 @@
 }
 \examples{
 # simple uses:
-mtcars |> head()                      # same as head(mtcars)
-mtcars |> head(2)                     # same as head(mtcars, 2)
+require(utils)
+mtcars |> head()               # same as head(mtcars)
+mtcars |> head(2)              # same as head(mtcars, 2)
 mtcars |> subset(cyl == 4) |> nrow()  # same as nrow(subset(mtcars, cyl == 4))
 
 # to pass the lhs into an argument other than the first, either

src/library/base/man/proc.time.Rd

@@ -66,7 +66,7 @@ proc.time()
 \examples{\donttest{
 ## a way to time an R expression: system.time is preferred
 ptm <- proc.time()
-for (i in 1:50) mad(stats::runif(500))
+for (i in 1:50) stats::mad(stats::runif(500))
 proc.time() - ptm
 }}
 \keyword{utilities}

src/library/base/man/qr.Rd

@@ -169,14 +169,14 @@ h9 \%*\% x              # = y
 
 
 ## overdetermined system
-A <- matrix(runif(12), 4)
+A <- matrix(stats::runif(12), 4)
 b <- 1:4
 qr.solve(A, b) # or solve(qr(A), b)
 solve(qr(A, LAPACK = TRUE), b)
 # this is a least-squares solution, cf. lm(b ~ 0 + A)
 
 ## underdetermined system
-A <- matrix(runif(12), 3)
+A <- matrix(stats::runif(12), 3)
 b <- 1:3
 qr.solve(A, b)
 solve(qr(A, LAPACK = TRUE), b)

src/library/base/man/rawConversion.Rd

@@ -113,6 +113,7 @@ stopifnot(exprs = {
   identical(packBits(       0:31) ,
             packBits(as.raw(0:31)))
 })
+require(utils)
 str(pBi <- packBits(intToBits(i)))
 data.frame(B = matrix(pBi, nrow=6, byrow=TRUE),
            hex = format(as.hexmode(i)), i)
@@ -147,7 +148,7 @@ bitC(1+2^-(1:53))# from 0.5 converge to 1
 d2bI <- function(x) vapply(as.double(x), function(x) intToBits(numToInts(x)), raw(64L))
 d2b  <- function(x) vapply(as.double(x), function(x)           numToBits(x) , raw(64L))
 set.seed(1)
-x <- c(sort(rt(2048, df=1.5)),  2^(-10:10), 1+2^-(1:53))
+x <- c(sort(stats::rt(2048, df=1.5)),  2^(-10:10), 1+2^-(1:53))
 str(bx <- d2b(x)) # a  64 x 2122  raw matrix
 stopifnot( identical(bx, d2bI(x)) )
 

src/library/base/man/regmatches.Rd

@@ -123,14 +123,15 @@ z
 
 ## With `perl = TRUE` and `invert = FALSE` capture group names
 ## are preserved.  Collect functions and arguments in calls:
+require(utils)
 NEWS <- head(readLines(file.path(R.home(), 'doc', 'NEWS.2')), 100)
 m <- gregexec("(?<fun>\\\\w+)\\\\((?<args>[^)]*)\\\\)", NEWS, perl = TRUE)
 y <- regmatches(NEWS, m)
 y[[16]]
 ## Make tabular, adding original line numbers
 mdat <- as.data.frame(t(do.call(cbind, y)))
 mdat <- cbind(mdat, line=rep(seq_along(y), lengths(y) / ncol(mdat)))
-head(mdat)
+utils::head(mdat)
 NEWS[head(mdat[['line']])]
 }
 \keyword{character}

src/library/base/man/substr.Rd

@@ -102,7 +102,7 @@ substring(x, 2, 4:6)
 X <- x
 names(X) <- LETTERS[seq_along(x)]
 comment(X) <- noquote("is a named vector")
-str(aX <- attributes(X))
+utils::str(aX <- attributes(X))
 substring(x, 2) <- c("..", "+++")
 substring(X, 2) <- c("..", "+++")
 X

src/library/base/man/textconnections.Rd

@@ -125,6 +125,7 @@ trt <- c(4.81, 4.17, 4.41, 3.59, 5.87, 3.83, 6.03, 4.89, 4.32, 4.69)
 group <- gl(2, 10, 20, labels = c("Ctl", "Trt"))
 weight <- c(ctl, trt)
 sink(zz)
+require(stats)
 anova(lm.D9 <- lm(weight ~ group))
 cat("\nSummary of Residuals:\n\n")
 summary(resid(lm.D9))

src/library/base/man/timezones.Rd

@@ -327,6 +327,7 @@ OlsonNames(tzdir = NULL)
 }
 
 \examples{
+require(utils)
 Sys.timezone()
 
 str(OlsonNames()) ## typically around six hundred names,

src/library/base/man/trace.Rd

@@ -255,7 +255,7 @@ require(stats)
 
 ##  Very simple use
 trace(sum)
-hist(rnorm(100)) # shows about 3-4 calls to sum()
+graphics::hist(rnorm(100)) # shows about 3-4 calls to sum()
 untrace(sum)
 
 ## Show how pt() is called from inside power.t.test():

src/library/base/man/warnings.Rd

@@ -89,7 +89,7 @@ for(w in -1:1) {
 }
 ## at the end prints all three warnings, from the 'option(warn = 0)' above
 options(ow) # reset to previous, typically 'warn = 0'
-tail(warnings(), 2) # see the last two warnings only (via '[' method)
+utils::tail(warnings(), 2) # see the last two warnings only (via '[' method)
 
 ## Often the most useful way to look at many warnings:
 summary(warnings())