Re: [Rd] Failed "make check" under Fedora Core 4 (PR#7979)

From: Martyn Plummer <plummer_at_iarc.fr>
Date: Thu 30 Jun 2005 - 09:39:16 GMT

On Wed, 2005-06-29 at 19:55 +0200, kent@darwin.eeb.uconn.edu wrote:
> I downloaded R v2.1.1 earlier this morning to compile under Fedora Core
> 4. It compiled without incident, but 'make check' failed. Below is the
> relevant part of its report. Is this a known problem?

It is known that gcc 4.0.0 is buggy. The current recommendation, from Brian Ripley, is to use gcc 3.4.4 instead. We are awaiting the bug-fix release gcc 4.0.1.

R compiled with the gcc 4.0.0 provided on FC4 does pass "make checkall".  My guess is that your locally compiled version does not have the patches applied by Red Hat.

Martyn

> I used a locally compiled version of GCC v4.0.0 that reports
>
> [kent@d89h102 R-2.1.1]$ gcc -v
> Using built-in specs.
> Target: i686-pc-linux-gnu
> Configured with: ../gcc-4.0.0/configure --enable-languages=c,c++,f95,java
> Thread model: posix
> gcc version 4.0.0
> [kent@d89h102 R-2.1.1]$
>
> Kent Holsinger
> kent@darwin.eeb.uconn.edu
>
> make[3]: Entering directory `/home/kent/source-arc/R-2.1.1/tests'
> running code in 'eval-etc.R' ... OK
> comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ...2a3,157
> > > #### eval / parse / deparse / substitute etc
> > >
> > > ##- From: Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk>
> > > ##- Subject: Re: source() / eval() bug ??? (PR#96)
> > > ##- Date: 20 Jan 1999 14:56:24 +0100
> > > e1 <- parse(text='c(F=(f <- .3), "Tail area" = 2 * if(f < 1) 30
> else 90)')[[1]]
> > > e1
> > c(F = (f <- 0.3), "Tail area" = 2 * if (f < 1) 30 else 90)
> > > str(eval(e1))
> > Named num [1:2] 0.3 60
> > - attr(*, "names")= chr [1:2] "F" "Tail area"
> > > mode(e1)
> > [1] "call"
> > >
> > > ( e2 <- quote(c(a=1,b=2)) )
> > c(a = 1, b = 2)
> > > names(e2)[2] <- "a b c"
> > > e2
> > c("a b c" = 1, b = 2)
> > > parse(text=deparse(e2))
> > expression(c("a b c" = 1, b = 2))
> > >
> > > ##- From: Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk>
> > > ##- Date: 22 Jan 1999 11:47
> > >
> > > ( e3 <- quote(c(F=1,"tail area"=pf(1,1,1))) )
> > c(F = 1, "tail area" = pf(1, 1, 1))
> > > eval(e3)
> > F tail area
> > 1.0 0.5
> > > names(e3)
> > [1] "" "F" "tail area"
> > >
> > > names(e3)[2] <- "Variance ratio"
> > > e3
> > c("Variance ratio" = 1, "tail area" = pf(1, 1, 1))
> > > eval(e3)
> > Variance ratio tail area
> > 1.0 0.5
> > >
> > >
> > > ##- From: Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk>
> > > ##- Date: 2 Sep 1999
> > >
> > > ## The first failed in 0.65.0 :
> > > attach(list(x=1))
> > > evalq(dim(x) <- 1,as.environment(2))
> > > dput(get("x", env=as.environment(2)), control="all")
> > structure(1, .Dim = as.integer(1))
> > >
> > > e <- local({x <- 1;environment()})
> > > evalq(dim(x) <- 1,e)
> > > dput(get("x",env=e), control="all")
> > structure(1, .Dim = as.integer(1))
> > >
> > > ### Substitute, Eval, Parse, etc
> > >
> > > ## PR#3 : "..." matching
> > > ## Revised March 7 2001 -pd
> > > A <- function(x, y, ...) {
> > + B <- function(a, b, ...) { match.call() }
> > + B(x+y, ...)
> > + }
> > > (aa <- A(1,2,3))
> > B(a = x + y, b = 3)
> > > all.equal(as.list(aa),
> > + list(as.name("B"), a = expression(x+y)[[1]], b = 3))
> > [1] TRUE
> > > (a2 <- A(1,2, named = 3)) #A(1,2, named = 3)
> > B(a = x + y, named = 3)
> > > all.equal(as.list(a2),
> > + list(as.name("B"), a = expression(x+y)[[1]], named = 3))
> > [1] TRUE
> > >
> > > CC <- function(...) match.call()
> > > DD <- function(...) CC(...)
> > > a3 <- DD(1,2,3)
> > > all.equal(as.list(a3),
> > + list(as.name("CC"), 1, 2, 3))
> > [1] TRUE
> > >
> > > ## More dots issues: March 19 2001 -pd
> > > ## Didn't work up to and including 1.2.2
> > >
> > > f <- function(...) {
> > + val <- match.call(expand.dots=F)$...
> > + x <- val[[1]]
> > + eval.parent(substitute(missing(x)))
> > + }
> > > g <- function(...) h(f(...))
> > > h <- function(...) list(...)
> > > k <- function(...) g(...)
> > > X <- k(a=)
> > > all.equal(X, list(TRUE))
> > [1] TRUE
> > >
> > > ## Bug PR#24
> > > f <- function(x,...) substitute(list(x,...))
> > > deparse(f(a, b)) == "list(a, b)" &&
> > + deparse(f(b, a)) == "list(b, a)" &&
> > + deparse(f(x, y)) == "list(x, y)" &&
> > + deparse(f(y, x)) == "list(y, x)"
> > [1] TRUE
> > >
> > > tt <- function(x) { is.vector(x); deparse(substitute(x)) }
> > > a <- list(b=3); tt(a$b) == "a$b" # tends to break when ...
> > [1] TRUE
> > >
> > >
> > > ## Parser:
> > > 1 <
> > + 2
> > [1] TRUE
> > > 2 <=
> > + 3
> > [1] TRUE
> > > 4 >=
> > + 3
> > [1] TRUE
> > > 3 >
> > + 2
> > [1] TRUE
> > > 2 ==
> > + 2
> > [1] TRUE
> > > ## bug till ...
> > > 1 !=
> > + 3
> > [1] TRUE
> > >
> > > all(NULL == NULL)
> > [1] TRUE
> > >
> > > ## PR #656 (related)
> > > u <- runif(1); length(find(".Random.seed")) == 1
> > [1] TRUE
> > >
> > > MyVaR <<- "val";length(find("MyVaR")) == 1
> > [1] TRUE
> > > rm(MyVaR); length(find("MyVaR")) == 0
> > [1] TRUE
> > >
> > >
> > > ## Martin Maechler: rare bad bug in sys.function() {or match.arg()}
> (PR#1409)
> > > callme <- function(a = 1, mm = c("Abc", "Bde")) {
> > + mm <- match.arg(mm); cat("mm = "); str(mm) ; invisible()
> > + }
> > > ## The first two were as desired:
> > > callme()
> > mm = chr "Abc"
> > > callme(mm="B")
> > mm = chr "Bde"
> > > mycaller <- function(x = 1, callme = pi) { callme(x) }
> > > mycaller()## wrongly gave `mm = NULL' now = "Abc"
> > mm = chr "Abc"
> make[3]: *** [eval-etc.Rout] Error 1
> make[3]: Leaving directory `/home/kent/source-arc/R-2.1.1/tests'
> make[2]: *** [test-Specific] Error 2
> make[2]: Leaving directory `/home/kent/source-arc/R-2.1.1/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/home/kent/source-arc/R-2.1.1/tests'
> make: *** [check] Error 2
>
> <<insert bug report here>>
>
>
>
> --please do not edit the information below--
>
> Version:
> platform = i686-pc-linux-gnu
> arch = i686
> os = linux-gnu
> system = i686, linux-gnu
> status =
> major = 2
> minor = 1.1
> year = 2005
> month = 06
> day = 20
> language = R
>
> Locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C
>
> Search Path:
> .GlobalEnv, package:methods, package:stats, package:graphics,
> package:grDevices, package:utils, package:datasets, Autoloads, package:base
>
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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Thu Jun 30 19:47:35 2005

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