NetBSD Problem Report #55328

From  Sun May 31 13:26:24 2020
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Date: Sun, 31 May 2020 13:26:22 +0000 (UTC)
Subject: math/R fails to build
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>Number:         55328
>Category:       pkg
>Synopsis:       math/R fails to build
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    pkg-manager
>State:          open
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Sun May 31 13:30:00 +0000 2020
>Last-Modified:  Wed Jul 15 06:20:01 +0000 2020
>Originator:     Jukka Ruohonen
>Release:        NetBSD 9.0_STABLE
System: NetBSD kafka 9.0_STABLE NetBSD 9.0_STABLE (GENERIC_KASLR) #0: Sun May 31 12:08:44 EEST 2020
jruoho@kafka:/usr/obj/sys/arch/amd64/compile/GENERIC_KASLR amd64
Architecture: x86_64 Machine: amd64
R-3.6.1 fails to build. The relevant trace is:

gmake[4]: Leaving directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src/library/tools'
gmake[4]: Entering directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src/library/tools'
installing 'sysdata.rda'

 *** caught segfault ***
address 0x608, cause 'memory not mapped'

19: get(name, envir = asNamespace(pkg), inherits = FALSE)
20: tools:::sysdata2LazyLoadDB
An irrecoverable exception occurred. R is aborting now ...
[1]   Done                    echo "tools:::sysdata2LazyLoadDB("./R/sysdata.... |
      Segmentation fault (core dumped) R_DEFAULT_PACKAGES=NULL LC_ALL=C R_ENABLE_JIT=...
gmake[4]: *** [../../../share/make/ sysdata] Error 139
gmake[4]: Leaving directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src/library/tools'
gmake[3]: *** [Makefile:36: all] Error 2
gmake[3]: Leaving directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src/library/tools'
gmake[2]: *** [Makefile:37: R] Error 1
gmake[2]: Leaving directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src/library'
gmake[1]: *** [Makefile:28: R] Error 1
gmake[1]: Leaving directory '/tmp/pkgsrc/math/R/work/R-3.6.1/src'
gmake: *** [Makefile:61: R] Error 1
*** Error code 2

Try to build the package.

From: Jukka Ruohonen <>
Subject: Re: pkg/55328: math/R fails to build
Date: Wed, 15 Jul 2020 09:16:22 +0300

 Fortunately, this issue is simpler than I feared. Thus, I will close this
 PR and file another one if and when I better understand what is wrong.

 In any case, the problem is related to unicode; R works fine on NetBSD with,
 e.g., LC_ALL="en_US.ISO8859-1".  However, with UTF-8 most functions that
 invoke graphical output systematically segfault. An example:

 $ locale
 $ R

 R version 3.6.1 (2019-07-05) -- "Action of the Toes"
 Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64--netbsd (64-bit)

 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 During startup - Warning message:
 Setting LC_COLLATE failed, using "C" 
 > hist(rnorm(3000))

  *** caught segfault ***
 address 0x64c, cause 'memory not mapped'

  1: tolower(breaks)
  2: match.arg(tolower(breaks), c("sturges", "fd", "freedman-diaconis", "scott"))
  3: hist.default(rnorm(3000))
  4: hist(rnorm(3000))

 Possible actions:
 1: abort (with core dump, if enabled)
 2: normal R exit
 3: exit R without saving workspace
 4: exit R saving workspace
 Selection: 1
 R is aborting now ...
 Memory fault (core dumped) 

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