File: C:/Program Files/R/R-4.4.0/tests/reg-packages.R
.R_LIBS <- function(libp = .libPaths()) { # (>> in utils?)
libp <- libp[! libp %in% .Library]
if(length(libp))
paste(libp, collapse = .Platform$path.sep)
else "" # character(0) is invalid for Sys.setenv()
}
.libPaths(tail(.libPaths(), 1), include.site=FALSE) # no extra libraries (w/ many pkgs)\n")
Sys.setenv(R_LIBS = .R_LIBS() # for build.pkg() & install.packages()
, R_BUILD_ENVIRON = "nothing" # avoid ~/.R/build.environ which might set R_LIBS
, R_ENVIRON = "none"
, R_PROFILE = "none"
)
showProc.time <- local({ ## function + 'pct' variable
pct <- proc.time()
function(final="\n") { ## CPU elapsed __since last called__
ot <- pct ; pct <<- proc.time()
cat('Time elapsed: ',
format.default(round((pct - ot)[1:3], digits=3), digits=4),
final)
}
})
options(
width = 120
, repos = character() # tests here should work without remote access
)
## PR 1271 detach("package:base") crashes R.
tools::assertError(detach("package:base"))
## invalid 'lib.loc'
stopifnot(length(installed.packages("mgcv")) == 0)
## gave a low-level error message
showProc.time()
## package.skeleton() with metadata-only code
## work in current (= ./tests/ directory):
tmp <- tempfile()
writeLines(c('setClass("foo", contains="numeric")',
'setMethod("show", "foo",',
' function(object) cat("I am a \\"foo\\"\\n"))'),
tmp)
if(file.exists("myTst")) unlink("myTst", recursive=TRUE)
package.skeleton("myTst", code_files = tmp)# with a file name warning
file.copy(tmp, (tm2 <- paste(tmp,".R", sep="")))
unlink("myTst", recursive=TRUE)
op <- options(warn=2) # *NO* "invalid file name" warning {failed in 2.7.[01]}:
package.skeleton("myTst", code_files = tm2)
options(op)
##_2_ only a class, no generics/methods:
writeLines(c('setClass("DocLink",',
'representation(name="character",',
' desc="character"))'), tmp)
if(file.exists("myTst2")) unlink("myTst2", recursive=TRUE)
package.skeleton("myTst2", code_files = tmp)
##- end_2_ # failed in R 2.11.0
stopifnot(1 == grep("setClass",
readLines(list.files("myTst/R", full.names=TRUE))),
c("foo-class.Rd","show-methods.Rd") %in% list.files("myTst/man"))
## failed for several reasons in R < 2.7.0
##
## Part 2: -- build, install, load and "inspect" the package:
build.pkg <- function(dir, destdir = NULL, ignore.stderr = FALSE, no.latex=TRUE) {
dir <- normalizePath(dir)
if(length(dir) > 1)
return(lapply(dir, build.pkg, destdir=destdir,
ignore.stderr=ignore.stderr, no.latex=no.latex))
## else one 'dir':
stopifnot(dir.exists(dir), file.exists(DESC <- file.path(dir, "DESCRIPTION")))
pkgName <- sub("^[A-Za-z]+: ", "", grep("^Package: ", readLines(DESC), value=TRUE))
patt <- paste(pkgName, ".*tar\\.gz$", sep="_")
unlink(dir('.', pattern = patt))
Rcmd <- paste(shQuote(file.path(R.home("bin"), "R")), "CMD")
r <- system(paste(Rcmd, "build --keep-empty-dirs",
if(no.latex) "--no-manual", shQuote(dir)),
ignore.stderr=ignore.stderr, intern = TRUE)
## return name of tar file built {plus the build log} :
tball <- structure(dir('.', pattern = patt), log3 = r)
if(is.null(destdir))
tball
else {
file.copy(tball, destdir)
file.path(destdir, basename(tball))
}
}
build.pkg("myTst")
## clean up any previous attempt (which might have left a 00LOCK)
unlink("myLib", recursive = TRUE)
dir.create("myLib")
install.packages("myTst", lib = "myLib", repos=NULL, type = "source")
print(installed.packages(lib.loc= "myLib", priority= "NA"))## (PR#13332)
stopifnot(require("myTst",lib = "myLib"))
sm <- findMethods(show, where= as.environment("package:myTst"))
stopifnot(sm@names == "foo")
unlink("myTst_*")
## test warnings for missing/autogenerated Rd content
owd <- setwd("myTst") # (currently) needed for \Sexpr macros
prompt(identity, filename = "man/identity.Rd")
print(res <- tools::checkRdContents(dir = "."))
stopifnot(exprs = {
res[["foo-class.Rd"]]$missing_description # was part of checkRd() in R < 4.4.0
identical(res[["identity.Rd"]]$arguments_with_no_description, "x")
## R < 4.4.0 treated \n and Rd comments as sufficient content
identical(res[["identity.Rd"]]$offending_autogenerated_content[,1], "\\title")
})
file.remove("man/identity.Rd")
setwd(owd)
## getPackageName() for "package:foo":
require('methods')
library(tools)
oo <- options(warn=2)
detach("package:tools", unload=TRUE)
options(oo)
## gave warning (-> Error) about creating package name
## More building & installing packages
## NB: tests were added here for 2.11.0.
## NB^2: do not do this in the R sources (but in a build != src directory!)
## and this testdir is not installed.
if(interactive() && Sys.getenv("USER") == "maechler")
Sys.setenv(SRCDIR = normalizePath("~/R/D/r-devel/R/tests"))
(pkgSrcPath <- file.path(Sys.getenv("SRCDIR"), "Pkgs"))# e.g., -> "../../R/tests/Pkgs"
## SRCDIR not available on windows, so pkgSrcPath won't be populated
## if this happens non-interactively, cleanup and quit gracefully
if(!file_test("-d", pkgSrcPath) && !interactive()) {
unlink("myTst", recursive=TRUE)
showProc.time()
q("no")
}
## else w/o clause:
showProc.time()
do.cleanup <- !nzchar(Sys.getenv("R_TESTS_NO_CLEAN"))
isWIN <- .Platform$OS.type == "windows"
has.symlink <- !isWIN
## Installing "on to" a package existing as symlink in the lib.loc
## -- used to fail with misleading error message (#PR 16725):
if(has.symlink && !unlink("myLib_2", recursive=TRUE) && dir.create("myLib_2") &&
file.rename("myLib/myTst", "myLib_2/myTst") &&
file.symlink("../myLib_2/myTst", "myLib/myTst"))
install.packages("myTst", lib = "myLib", repos=NULL, type = "source")
## In R <= 3.3.2 gave error with *misleading* error message:
## ERROR: ‘myTst’ is not a legal package name
if(isWIN) { # (has no symlinks anyway)
file.copy(pkgSrcPath, tempdir(), recursive = TRUE)
} else { # above file.copy() not useful as it replaces symlink by copy
system(paste('cp -R', shQuote(pkgSrcPath), shQuote(tempdir())))
}
pkgPath <- file.path(tempdir(), "Pkgs")
if(!dir.exists(pkgPath)) {
message("No valid 'pkgPath' (from 'pkgSrcPath') - exit this test")
if(!interactive()) q("no")
}
## pkgB tests an empty R directory
dir.create(file.path(pkgPath, "pkgB", "R"), recursive = TRUE,
showWarnings = FALSE)
## (how can this happen reliably more easily?)
##' Copy directory d1 to *(newly created |cleaned)* directory d2 -- also with*in* same directory
##' "cp -a d1/ d2/"
dirCopy <- function(d1, d2) {
stopifnot(exprs = {
length(d1) == length(d2) ; length(d1) == 1L
dir.exists(d1)
dir.exists(D2 <- dirname(d2)) || dir.create(D2, recursive=TRUE)
!dir.exists(d2) || unlink(d2, recursive=TRUE) == 0
## unbelievable contortion just so it works within the *same* directory (really ??)
## 1. copy to *other dir* :
dir.create(tD <- tempfile("dirCp"))
file.copy(d1, tD, recursive = TRUE)
## 2. correctly "rename" ( i.e., *move*) to "this" dir:
file.rename(file.path(tD, basename(d1)),
file.path(D2, basename(d2)))
})
}
##
## pkgB{2,3} := pkgB but with missing/incomplete 'Imports:' entry in DESCRIPTION
pBp <- file.path(pkgPath, "pkgB")
dirCopy(pBp, pB2p <- file.path(pkgPath, "pkgB2"))
dirCopy(pBp, pB3p <- file.path(pkgPath, "pkgB3"))
if(okB2 <- file.exists(DN <- file.path(pB2p, "DESCRIPTION"))) {
Dlns <- readLines(DN); i <- grep("^Imports:", Dlns)
## drop 'Imports: ' completely (and replace [Pp]kgB by [Pp]kgB2):
writeLines(gsub("kgB", "kgB2", Dlns[-i]), con = DN)
}
if(okB3 <- file.exists(DN <- file.path(pB3p, "DESCRIPTION"))) {
Dlns <- readLines(DN); i <- grep("^Imports:", Dlns)
## Only keep the first 'Imports: ' (and replace [Pp]kgB by [Pp]kgB3):
Dlns[i] <- sub(",.*", "", Dlns[i])
writeLines(gsub("kgB", "kgB3", Dlns), con = DN)
}
## PR17859.3 := PR17859.2, but with missing '}' in <pkg>/R/f3.3 :
pP2 <- file.path(pkgPath, "PR17859.2"); f2nm <- file.path(pP2, "R", "f3.R")
pP3 <- file.path(pkgPath, "PR17859.3"); f3nm <- file.path(pP3, "R", "f3.R")
dirCopy(pP2, pP3); DN <- "DESCRIPTION" # --> fix up pkg name
writeLines(sub("^(Package: .*)\\.2$", "\\1.3", readLines(file.path(pP2, DN))),
file.path(pP3, DN))
f3lns <- f2lns <- readLines(f2nm)
iBrace <- grep("closing brace", f2lns, fixed=TRUE)
(f3lns[iBrace] <- sub("^", "#> ", f2lns[iBrace]))
(writeLines(f3lns, f3nm))
p.fails <- paste0("PR17859.", 1:3)
io859 <- c("--no-help", "--no-test-load", "--no-byte-compile")
InstOpts <- list("exSexpr" = "--html"
, "parseDataEx" = c("--with-keep.parse.data", "--with-keep.source", "--install-tests")
)
for(p in p.fails) InstOpts <- c(InstOpts, `names<-`(list(io859), p))
p.lis <- c(if("Matrix" %in% row.names(installed.packages(.Library)))
c("pkgA", "pkgB", if(okB2) "pkgB2", if(okB3) "pkgB3", "pkgC"),
"PR17501",
"parseDataEx", # PR16756
p.fails,
"S3export",
"exNSS4", "exNSS4nil", "exSexpr")
p.lis; (pBlis <- grep("^pkgB", p.lis, value=TRUE))
pkgApath <- file.path(pkgPath, "pkgA")
if("pkgA" %in% p.lis && !dir.exists(d <- pkgApath)) {
# on Windows, 'pkgA' may end up being a text file with a single line
# with a note it is meant to be a link to xDir/pkg
cat("symlink 'pkgA' does not exist as directory ",d,"; copying it\n", sep='')
unlink(d, recursive=TRUE)
dir.create(d) # ensure it is a single existing directory
pkgdir <- file.path(pkgPath, "xDir", "pkg")
file.copy(file.path(pkgdir, list.files(pkgdir)), to = d, recursive=TRUE)
## if even the copy failed (NB: pkgB, pkgC depend on pkgA)
if(!dir.exists(d)) p.lis <- p.lis[!(p.lis %in% c("pkgA", pBlis, "pkgC"))]
}
dir2pkg <- function(dir) sub("^pkgC", "PkgC", dir)
if(is.na(match("myLib", .lP <- .libPaths()))) {
.libPaths(c("myLib", .lP)) # PkgC needs pkgA from there
.lP <- .libPaths()
}
Sys.setenv(R_LIBS = .R_LIBS(.lP)) # for build.pkg() & install.packages()
showProc.time()
for(p in p.lis) {
p. <- dir2pkg(p) # 'p' is sub directory name; 'p.' is package name
cat("===--===\nFrom pkgPath sub directory", p, " building package", p., "...\n")
pkgP <- file.path(pkgPath, p)
r <- build.pkg(pkgP, ignore.stderr = (p != "exSexpr")) # 1-2 sec
showProc.time()
if(!length(r)) # so some sort of failure, show log
cat(attr(r, "log3"), sep = "\n")
if(!isTRUE(file.exists(r)))
stop("R CMD build failed (no tarball) for package ", p.)
if(p %in% pBlis) { ## R CMD check "dependencies"
res <- tools:::.check_package_depends(dir=pkgP, force_suggest=FALSE)
cat("check_package_depends:\n") ; print(res)
if(length(res)) pres <- capture.output(res)
switch(p
, "pkgB" = stopifnot(length(res) == 0)
, "pkgB2" = stopifnot(exprs = {
length(res) == 1
identical(res$missing_namespace_depends, c("methods", "pkgA"))
grepl("Namespace dependencies .* DESCRIPTION" , pres[1])
})
, "pkgB3" = stopifnot(exprs = {
length(res) == 1
identical(res[[1]], "pkgA")
grepl("Namespace dependency .* DESCRIPTION" , pres[1])
})
)
showProc.time()
} else if(p %in% p.fails) {
## NB: Fail with *parse* errors which are *not* tryCatch-able ==> need to call R
## tryCatch(error = identity,
## install.packages(r, lib = "myLib", repos=NULL, type = "source",
## INSTALL_opts = InstOpts[[p.]])) -> err
## cat("tryCatch gave "); dput(err)
## stopifnot(inherits(err, "error"))
## FIXME: do a bit more
tf <- tempfile(paste0("regP-inst_",p))
status <- tools:::run_Rcmd(c("INSTALL", r, InstOpts[[p.]]),
out=tf, timeout = 10)
writeLines(errlns <- readLines(tf))
stopifnot(exprs = {
status > 0 # see status == 1L
length(iE <- grep("Error in parse(", errlns, fixed=TRUE)) > 0
local({
parseM1 <- "(syntax error|unexpected symbol)" # may depend on bison version
parseM2 <- "(syntax error|unexpected end of input)" # (ditto)
switch(p
, "PR17859.1" = grepl(paste0(p, "/R/f2.R:3:[0-9]+: ", parseM1), errlns[iE+1])
, "PR17859.2" =
, "PR17859.3" = grepl(paste0(p, "/R/f2.R:6:0: ", parseM2), errlns[iE+1])
, stop("invalid package p=", p))
})
})
next # pkg in for(...)
}
## otherwise install the tar file:
cat("installing package", p., "using built file", r, "...\n")
## "FIXME": want to catch warnings in the "console output" of this,
## e.g. exNSS4nil, "S4 exports specified in 'NAMESPACE' but not defined .."
## and exSexpr, "nestedSexpr.Rd:5: unprocessed 'build' macro from install-stage \Sexpr"
install.packages(r, lib = "myLib", repos=NULL, type = "source",
INSTALL_opts = InstOpts[[p.]])
stopifnot(require(p., lib = "myLib", character.only=TRUE))
detach(pos = match(p., sub("^package:","", search())))
showProc.time()
}
cat("\n -------------------end { for(p in p.lis) }----------------------------\n")
(res <- installed.packages(lib.loc = "myLib", priority = "NA"))
(p.lis <- dir2pkg(setdiff(p.lis, p.fails))) # --> *package* names of installed pkgs
stopifnot(exprs = {
identical(res[,"Package"], setNames(, sort(c(p.lis, "myTst"))))
res[,"LibPath"] == "myLib"
})
### Specific Tests on our "special" packages: ------------------------------
tf <- tempfile("chk_donttest")
## why does this not work (not catch stderr)? textConnection("checkTxt", open="w")
system.time(status <-
tools:::run_Rcmd(c("check", "PR17501_1.0.tar.gz", "--no-manual"),
out = tf,
## avoid delays/timeouts with a broken network route:
env = c("R_REPOSITORIES=NULL"), # (no cyclic dep check)
timeout = 50))# see 5--7 sec; Solaris needed > 30
stopifnot(exprs = {
status == 1 # an ERROR now
is.character(exLines <-
readLines(file.path("PR17501.Rcheck", "PR17501-Ex.R")))
{ str(exLines); length(exLines) > 20 } # str(): diagnostic in case
is.integer(i <- grep("^R\\.Version\\( *# missing closing paren", exLines))
grepl("^## No test", exLines[i-1])
{ str(tlines <- readLines(tf)); length(tlines) > 20 }
length(iw <- grep("^Warning: parse error", tlines)) == 1
(lenN <- length(print(iN <- grep("^[1-9][0-9]:", tlines)))) >= 2
iN - iw == seq_len(lenN) # these (3) lines come immediately after 'Warning',
## and "related" to the some 'missing .. paren' above:
!is.na(ierr <- as.integer(substr(print(tlines[iN[1]]), 1, 2)))
8 <= print(ierr - i) & ierr - i <= 14 # see 11
}) ## failed in R <= 4.1.1
str(ok <- tryCatch(warning=conditionMessage, require("S3export")))
## gave "S3 method 'within.list' was declared in NAMESPACE but not found"
ml <- myList(list(x = 1, y = 2:5, c = list(L = letters[1:4], "foo")))
## Check that the S3 method for within() works {defined in NAMESPACE only!}
stopifnot(ok, inherits(ml, "myList"),
"within.myList" %in% as.character(methods(within)),
is.list(r <- within(ml, sum <- x+y)), r$sum == 3:6)
## These used to fail because of the sym.link in pkgA
if("pkgA" %in% p.lis && dir.exists(pkgApath)) {
cat("undoc(pkgA):\n"); print(uA <- tools::undoc(dir = pkgApath))
cat("codoc(pkgA):\n"); print(cA <- tools::codoc(dir = pkgApath))
cat("extends(\"classApp\"):\n"); print(ext.cA <- extends("classApp"))
stopifnot(exprs = {
identical(uA$`code objects`, c("nil", "search"))
identical(uA$`data sets`, "nilData")
## pkgC's class union is now (after loading pkgC) also visible in the "classApp" subclass
## (which gave warning). ==> warning "wrong": somehow it *did* get updated:
"numericA" %in% ext.cA
})
} else message("'pkgA' not available")
showProc.time()
## - Check conflict message.
## - Find objects which are NULL via "::" -- not to be expected often
## we have one in our pkgA, but only if Matrix is present.
if(dir.exists(file.path("myLib", "pkgA"))) {
msgs <- capture.output(require(pkgA, lib="myLib"), type = "message")
writeLines(msgs)
stopifnot(length(msgs) > 2,
length(grep("The following object is masked.*package:base", msgs)) > 0,
length(grep("\\bsearch\\b", msgs)) > 0)
data(package = "pkgA") # -> nilData
stopifnot(is.null( pkgA:: nil),
is.null( pkgA::: nil),
is.null( pkgA:: nilData)) # <-
## R-devel (pre 3.2.0) wrongly errored for NULL lazy data
## ::: does not apply to data sets:
tools::assertError(is.null(pkgA:::nilData))
} else message("'pkgA' not in 'myLib'")
showProc.time()
## Check error from invalid logical field in DESCRIPTION:
(okA <- ("pkgA" %in% p.lis) && dir.exists(pkgApath) &&
file.exists(DN <- file.path(pkgApath, "DESCRIPTION")))
if(okA) {
Dlns <- readLines(DN); i <- grep("^LazyData:", Dlns)
Dlns[i] <- paste0(Dlns[i], ",") ## adding a ","
writeLines(Dlns, con = DN)
## do not test installation failure in myLib as previous pkgA would be removed
## from there (because no.q=TRUE causes do_exit_on_error() to be called twice)
## and if getNamespaceInfo("pkgA", "path") no longer exists,
## sessionInfo() fails in the "exSexpr" test below
instEXPR <- quote(
tools:::.install_packages(c("--clean", paste0("--library=", tempdir()), pkgApath), no.q = TRUE)
) ## ----------------- ----
if(interactive()) { ## << "FIXME!" This (sink(.) ..) fails, when run via 'make'.
## install.packages() should give "the correct" error but we cannot catch it
## One level lower is not much better, needing sink() as capture.output() fails
ftf <- file(tf <- tempfile("inst_pkg"), open = "wt")
sink(ftf); sink(ftf, type = "message")# "message" should be sufficient
eval(instEXPR)
sink(type="message"); sink()## ; close(ftf); rm(ftf)# end sink()
writeLines(paste(" ", msgs <- readLines(tf)))
message(err <- grep("^ERROR:", msgs, value=TRUE))
stopifnot(exprs = {
length(err) > 0
grepl("invalid .*LazyData .*DESCRIPTION", err)
})
} else {
message("non-interactive -- tools:::.install_packages(..) : ")
## show the error message in the *.Rout file and assert failure
stopifnot(inherits(try( eval(instEXPR) ), "try-error"))
}
} else message("pkgA/DESCRIPTION not available")
showProc.time()
## R CMD check should *not* warn about \Sexpr{} built sections in Rd (PR#17479):
writeLines(msg <- capture.output(
tools:::.check_package_parseRd(dir = file.path(pkgPath, "exSexpr"),
minlevel = -Inf)
))
if(length(ifoo <- grep("foo.Rd", msg, fixed = TRUE)))
stop(".check_package_parseRd() complained about foo.Rd in\n",
paste0(msg[ifoo], collapse = "\n"))
## in R <= 3.5.1, gave
## "prepare_Rd: foo.Rd:14: Section \\Sexpr is unrecognized and will be dropped"
## nor should it spuriously warn about LIST-wrapped \Sexpr Rd results
## (when _R_CHECK_RD_CHECKRD_MINLEVEL_=-Inf)
if(length(ibraces <- grep("a\\.Rd.* braces", msg)))
stop(".check_package_parseRd() found unnecessary braces")
## in R <= 4.3.1, gave,
##checkRd: (-3) file '..../man/a.Rd': Unnecessary braces at '{a1....
## but R >= 4.4.0 *does warn* about badly nested Sexpr macros
## and about Rd macros in \Sexpr code (e.g., #ifdef inside build stage macro)
stopifnot(exprs = {
any(grepl("nestedSexpr.Rd:5: unprocessed", msg, fixed = TRUE))
any(grepl("nestedDefines.Rd:9-16: \\Sexpr expects R", msg, fixed = TRUE))
})
## the rendered help outputs such unprocessed macros verbatim
installedRdDB <- tools::Rd_db("exSexpr", lib.loc = "myLib")
writeLines(helptxt <- capture.output(
tools::Rd2txt(installedRdDB[["nestedSexpr.Rd"]],
options = list(underline_titles = FALSE))
))
stopifnot(exprs = {
grepl("\\Sexpr[stage=build]{", helptxt[5], fixed = TRUE) # unprocessed
grepl(as.character(getRversion()), helptxt[9], fixed = TRUE) # processed
})
## FIXME: the partial Rd DB is built with c("unix", "windows") defines, so
## conditional defines are currently ineffective in help pages with build macros
## i.e., the following is FALSE (the \seealso section is always included)
any(grepl("See Also:", helptxt, fixed = TRUE)) == (.Platform$OS.type == "windows")
## post-build macros can contain conditional defines
tools::Rd2txt(installedRdDB[["nestedDefinesOK.Rd"]])
deparsedLines <- as.character(installedRdDB[["nestedDefinesOK.Rd"]])
stopifnot(("unix" %in% deparsedLines) == (.Platform$OS.type == "unix"),
("windows" %in% deparsedLines) == (.Platform$OS.type == "windows"))
## R < 4.4.0 did not process \Sexpr macros containing #ifdef conditionals
## \packageAuthor knows about Authors@R
stopifnot(print(tools:::.Rd_get_section(installedRdDB[["foo.Rd"]], "author")) |>
grepl(pattern = "R Core Team", fixed = TRUE) |> any())
## gave \author{NA} in R <= 4.3.1
showProc.time()
if(dir.exists(file.path("myLib", "exNSS4"))) withAutoprint({
require("exNSS4", lib="myLib")
validObject(dd <- new("ddiM"))
print(is(dd)) # 5 of them ..
writeLines(myGmeth <- capture.output(show(exNSS4:::myGenf)))
stopifnot(exprs = {
is(dd, "mM")
inherits(dd, "mM")
grepl("showMethods(exNSS4:::myGenf)", myGmeth[length(myGmeth)], fixed=TRUE)
})
## tests here should *NOT* assume recommended packages,
## let alone where they are installed
if(dir.exists(file.path(.Library, "Matrix"))) {
for(ns in c(rev(p.lis), "Matrix")) unloadNamespace(ns)
## Both exNSS4 and Matrix define "atomicVector" *the same*,
## but 'exNSS4' has it extended - and hence *both* are registered in cache -> "conflicts"
requireNamespace("exNSS4", lib= "myLib")
## Found in cache, since there is only one definition.
## Might confuse users.
stopifnot(isVirtualClass(getClass("atomicVector")))
requireNamespace("Matrix", lib= .Library)
## Throws an error, because there is ambiguity in the cache,
## and the dynamic search will not find anything, since the packages
## are not attached.
tools::assertCondition(
acl <- getClass("atomicVector")
)
## Once Matrix is attached, we find a unique definition.
library(Matrix)
stopifnot(isVirtualClass(getClass("atomicVector")))
}
})
showProc.time()
require("parseDataEx", lib="myLib") # installed with --install-tests :
stopifnot(dir.exists(tdir <- system.file(package="parseDataEx", "tests")))
## run the tests/*.R
invisible( lapply(dir(tdir, pattern="[.]R$", full.names = TRUE), source) )
showProc.time()
## Part 3: repository construction ---------------------------------------------
## test tools::write_PACKAGES and tools::update_PACKAGES
oldpkgdir <- file.path(tempdir(), "pkgfiles/old")
newpkgdir <- file.path(tempdir(), "pkgfiles/new")
repodir <- file.path(tempdir(), "pkgrepo")
dir.create(oldpkgdir, recursive = TRUE)
dir.create(newpkgdir)
if(file.exists(repodir))
unlink(repodir, recursive = TRUE)
dir.create(repodir)
ro <- build.pkg(file.path(pkgPath, c("pkgD", "pkgB")), oldpkgdir)
rn <- build.pkg(file.path(pkgPath, c("pkgD_2", "pkgD_3")), newpkgdir)
unlist(ro)
unlist(rn)
##' A repo package database in directory 'dir'
mkPkgfiles <- function(dir)
file.path(dir, c("PACKAGES",
"PACKAGES.gz",
"PACKAGES.rds"))
##' safe read.dcf()
read.safe.dcf <- function(f) if(file.exists(f)) read.dcf(f) # else NULL
## this will fail with an error if write_PACKAGES
## and update_PACKAGES do not generate the same
## PACKAGE file entries, in the same order, with
## the same field order.
docompare <- function(..., repdir = repodir, strict = TRUE) {
Pfiles <- mkPkgfiles(repdir)
backupPfiles <- file.path(tempdir(), basename(Pfiles))
indfile <- Pfiles[1]
## vvvvvvvvvvvvvvv
tools::write_PACKAGES(repdir, type = "source", ...)
wpres <- read.safe.dcf(indfile) # write_P result
## reset the PACKAGES files so that update_PACKAGES thinks any deviations are "new"
if(all(file.exists(backupPfiles)))
file.copy(backupPfiles, Pfiles, overwrite = TRUE)
## vvvvvvvvvvvvvvv
tools::update_PACKAGES(repdir, type = "source", strict=strict, ...)
upres <- read.safe.dcf(indfile) # update_P result
stopifnot(identical(wpres, upres))
}
Pfiles <- mkPkgfiles(repodir)
backupPfiles <- file.path(tempdir(), basename(Pfiles))
if(all(file.exists(backupPfiles)))
unlink(backupPfiles)
showProc.time()
## test write_PACKAGES and update_PACKAGES
## on empty dir
## IGNORE_RDIFF_BEGIN
docompare() ## one warning expected, has a temp path in it so ignore diff
## IGNORE_RDIFF_END
oldpfs <- list.files(oldpkgdir, pattern = "\\.tar\\.gz$", recursive = TRUE, full.names = TRUE)
newpfs <- list.files(newpkgdir, pattern = "\\.tar\\.gz$", recursive = TRUE, full.names = TRUE)
## generate and backup "original repo state"
file.copy(oldpfs, to = repodir)
tools::write_PACKAGES(repodir, type = "source")
file.copy(Pfiles, backupPfiles, overwrite = TRUE)
showProc.time()
## test update_PACKAGES with no change
docompare()
## all old files gone, new files present
unlink(file.path(repodir, basename(oldpfs)))
file.copy(newpfs, to = repodir)
docompare()
docompare(strict=FALSE)
## put old ones back
file.copy(oldpfs, to = repodir)
showProc.time()
if(isWIN){
nrepodir <- normalizePath(repodir)
if(grepl("^\\\\", nrepodir)) #\\laptop\whatever
repourl <- paste0("file:", gsub("\\\\", "/", nrepodir))
else #C:\whatever
repourl <- paste0("file:///", gsub("\\\\", "/", nrepodir))
} else
repourl <- paste0("file://", normalizePath(repodir))
## make sure the ordering is right when
## old and new entries are mixed in final db
##
##' care: stopifnot(nrow(1) == 2) # does *not* trigger
checkMatrix <- function(x, n) stopifnot(is.matrix(x), nrow(x) == n)
docompare(latestOnly = TRUE)
str(ap <- available.packages(repourl, filters = list()))
checkMatrix(ap, 2)
docompare(latestOnly = FALSE)
str(ap <- available.packages(repourl, filters = list()))
checkMatrix(ap, 4)
docompare(latestOnly = TRUE, strict = FALSE)
str(ap <- available.packages(repourl, filters = list()))
checkMatrix(ap, 2)
docompare(latestOnly = FALSE, strict = FALSE)
str(ap <- available.packages(repourl, filters = list()))
checkMatrix(ap, 4)
## clean up
rmL <- c("myLib", if(has.symlink) "myLib_2", "myTst", "myTst2",
"PR17501.Rcheck")
if(do.cleanup) {
for(nm in rmL) unlink(nm, recursive = TRUE)
} else {
cat("Not cleaning, i.e., keeping ", paste(rmL, collapse=", "), "\n")
}
showProc.time()
## And the final:
environment(showProc.time)[["pct"]]