From plummer at iarc.fr  Thu Jun 30 11:39:16 2005
From: plummer at iarc.fr (Martyn Plummer)
Date: Thu, 30 Jun 2005 11:39:16 +0200
Subject: [Rd] Failed "make check" under Fedora Core 4 (PR#7979)
In-Reply-To: <20050629175526.AF68AA237@slim.kubism.ku.dk>
References: <20050629175526.AF68AA237@slim.kubism.ku.dk>
Message-ID: <1120124356.3564.5.camel@seurat>

On Wed, 2005-06-29 at 19:55 +0200, kent at 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 check-
all". 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 at 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 at d89h102 R-2.1.1]$
> 
> Kent Holsinger
> kent at 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 at 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 at 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 at 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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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