R help - May 2024 - grDevices segfault when building R4.4.0 on RHEL 9.1.

Hi all,

I seem to be getting segfaults when attempting to build R 4.4.0 on RHEL 9.1
(5.14.0-162.23.1.el9_1.x86_64). Interestingly, it seems to build ok on Rocky 9.1
and 9.3. This is the trace:


make[3]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

building package 'grDevices'

make[4]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

all.R is unchanged

make[4]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

make[4]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

make[5]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src'

make[6]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src'

../../../../library/grDevices/libs/grDevices.so is unchanged

make[7]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[8]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[9]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[9]: 'cairo.so' is up to date.

make[9]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[8]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[7]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src/cairo'

make[6]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src'

make[5]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices/src'

make[4]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

make[4]: Entering directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'
byte-compiling package 'grDevices'


 *** caught segfault ***

address 0x1801fa8f70, cause 'memory not mapped'


Traceback:

 1: solve.default(rgb)

 2: solve(rgb)

 3: drop(whitexyz %*% solve(rgb))

 4: make.rgb(red = c(0.625, 0.34), green = c(0.28, 0.595), blue = c(0.155,    
0.07), gamma = 1.8, white = "D65", name = "Apple RGB")

 5: eval(exprs[i], envir)

 6: eval(exprs[i], envir)

 7: sys.source(codeFile, env, keep.source = keep.source, keep.parse.data =
keep.parse.data)

 8: doTryCatch(return(expr), name, parentenv, handler)

 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])

10: tryCatchList(expr, classes, parentenv, handlers)

11: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if
(!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))         
call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)       
prefix <- paste("Error in", dcall, ": ")        LONG
<- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]   
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type =
"w")        if (is.na(w))             w <- 14L + nchar(dcall, type
= "b") + nchar(sm[1L],                 type = "b")        if
(w > LONG)             prefix <- paste0(prefix, "\n  ")    }   
else prefix <- "Error : "    msg <- paste0(prefix,
conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if
(!silent && isTRUE(getOption("show.error.messages"))) {       
cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }   
invisible(structure(msg, class = "try-error", condition = e))})

12: try(sys.source(codeFile, env, keep.source = keep.source, keep.parse.data =
keep.parse.data))

13: loadNamespace(package = package, lib.loc = lib.loc, keep.source =
keep.source,     keep.parse.data = keep.parse.data, partial = TRUE)

14: withCallingHandlers(expr, packageStartupMessage = function(c)
tryInvokeRestart("muffleMessage"))

15: suppressPackageStartupMessages(loadNamespace(package = package,     lib.loc
= lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data,    
partial = TRUE))

16: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,    
keep.parse.data = keep.parse.data, compress = compress, set.install.dir =
set.install.dir)

17: tools:::makeLazyLoading("grDevices")

An irrecoverable exception occurred. R is aborting now ...

make[4]: *** [../../../share/make/lazycomp.mk:9:
../../../library/grDevices/R/grDevices.rdb] Error 139

make[4]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

make[3]: *** [Makefile:28: all] Error 2

make[3]: Leaving directory
'/home/esteva.m/R/R-4.4.0/src/library/grDevices'

make[2]: *** [Makefile:39: R] Error 1

make[2]: Leaving directory '/home/esteva.m/R/R-4.4.0/src/library'

make[1]: *** [Makefile:28: R] Error 1

make[1]: Leaving directory '/home/esteva.m/R/R-4.4.0/src'

make: *** [Makefile:62: R] Error 1


Has anyone run into this?

cairo-1.17.4-7.el9.x86_64
cairo-gobject-1.17.4-7.el9.x86_64
cairo-devel-1.17.4-7.el9.x86_64
cairo-gobject-devel-1.17.4-7.el9.x86_64
pango-1.48.7-3.el9.x86_64
pango-devel-1.48.7-3.el9.x86_64

Cheers,


Miguel Esteva


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	[[alternative HTML version deleted]]

Dear Miguel Esteva,

I couldn't get a Red Hat "ubi9" container to install enough
dependencies to build R. Is there a way to reproduce your setup on a
virtual machine somewhere?

On Fri, 3 May 2024 00:42:43 +0000
Miguel Esteva via R-help <r-help at r-project.org> wrote:
>  *** caught segfault ***
> 
> address 0x1801fa8f70, cause 'memory not mapped'
> 
> 
> Traceback:
> 
>  1: solve.default(rgb)
This seems to crash inside the BLAS. Which BLAS are you using? Any
custom ./configure arguments? Which compilers are you running?

To find out more information about the crash, try to follow it with a
debugger. Change directory to src/library/grDevices and run:

_R_COMPILE_PKGS_=1 R_COMPILER_SUPPRESS_ALL=1 \
 R_DEFAULT_PACKAGES=NULL LC_ALL=C \
../../../bin/R -d gdb --vanilla --no-echo -e \
 'tools:::makeLazyLoading("grDevices")'

(This assumes building straight from the source directory. Adjust the
paths if you're using a separate build directory.)

Use the "run" command to start the process. One you see a crash, use
"backtrace" to see the state of the call stack at the place of the
crash, or "backtrace full" to include the contents of local variables.
The first few entries are probably the most important ones.

Not sure what to do with this information yet, but it might provide
more clues.

-- 
Best regards,
Ivan