R devel - Jun 2005 - Failed "make check" under Fedora Core 4 (PR#7979)

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?

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

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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