NetBSD Problem Report #56696
From mlelstv@arnold.localdomain Sun Feb 6 23:59:39 2022
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by mollari.NetBSD.org (Postfix) with ESMTPS id 24E5D1A9239
for <gnats-bugs@gnats.NetBSD.org>; Sun, 6 Feb 2022 23:59:39 +0000 (UTC)
Message-Id: <20220206235933.C2788BC141@arnold.localdomain>
Date: Mon, 7 Feb 2022 00:59:33 +0100 (CET)
From: mlelstv@serpens.de
Reply-To: mlelstv@serpens.de
To: gnats-bugs@NetBSD.org
Subject: R-tcltk2 build loops infinitely
X-Send-Pr-Version: 3.95
>Number: 56696
>Category: pkg
>Synopsis: R-tcltk2 build loops infinitely
>Confidential: no
>Severity: serious
>Priority: low
>Responsible: pkg-manager
>State: open
>Class: sw-bug
>Submitter-Id: net
>Arrival-Date: Mon Feb 07 00:00:00 +0000 2022
>Last-Modified: Mon Jun 20 07:40:01 +0000 2022
>Originator: Michael van Elst
>Release: NetBSD 9.2_STABLE
>Organization:
>Environment:
System: NetBSD slowpoke 9.2_STABLE NetBSD 9.2_STABLE (SLOWPOKE)
Architecture: x86_64
Machine: amd64
>Description:
Building R-tcltk2 ends in an R process looping infinitely, printing:
13863 13863 R read(0x9, 0x73d69846a980, 0x4000) = 188
"error reading package index file /pbulk/work/devel/R-tcltk2/work/.des"
>How-To-Repeat:
Build R-tcltk2
>Fix:
>Audit-Trail:
From: "Thomas Klausner" <wiz@netbsd.org>
To: gnats-bugs@gnats.NetBSD.org
Cc:
Subject: PR/56696 CVS commit: pkgsrc/devel/R-tcltk2
Date: Mon, 28 Mar 2022 15:51:46 +0000
Module Name: pkgsrc
Committed By: wiz
Date: Mon Mar 28 15:51:46 UTC 2022
Modified Files:
pkgsrc/devel/R-tcltk2: Makefile
Log Message:
R-tcltk2: mark as BROKEN
Infinite loop during build, see PR pkg/56696.
To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/devel/R-tcltk2/Makefile
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
From: Thomas Klausner <wiz@NetBSD.org>
To: NetBSD bugtracking <gnats-bugs@NetBSD.org>
Cc:
Subject: Re: pkg/56696: R-tcltk2 build loops infinitely
Date: Tue, 29 Mar 2022 19:52:27 +0200
On Mon, Feb 07, 2022 at 12:00:01AM +0000, Michael van Elst wrote:
> >Number: 56696
> >Category: pkg
> >Synopsis: R-tcltk2 build loops infinitely
mef's bulk build has more output about this than I've seen so far:
http://www.ki.nu/pkgsrc/reports/current/NetBSD-9.0/20220327.0453/R-tcltk2-1.2.11nb2/install.log
** testing if installed package can be loaded from temporary location
Warning: no DISPLAY variable so Tk is not available
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?)
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: can't find package tile
error reading package index file /tmp/devel/R-tcltk2/work/.destdir/usr/pkg/lib/R/library/00LOCK-tcltk2/00new/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?)
...
From: "Benny Siegert" <bsiegert@netbsd.org>
To: gnats-bugs@gnats.NetBSD.org
Cc:
Subject: PR/56696 CVS commit: [pkgsrc-2022Q1] pkgsrc/devel/R-tcltk2
Date: Fri, 1 Apr 2022 18:56:14 +0000
Module Name: pkgsrc
Committed By: bsiegert
Date: Fri Apr 1 18:56:13 UTC 2022
Modified Files:
pkgsrc/devel/R-tcltk2 [pkgsrc-2022Q1]: Makefile
Log Message:
Pullup ticket #6607 - requested by wiz
devel/R-tcltk2: mark as broken (infinite loop)
Revisions pulled up:
- devel/R-tcltk2/Makefile 1.5
---
Module Name: pkgsrc
Committed By: wiz
Date: Mon Mar 28 15:51:46 UTC 2022
Modified Files:
pkgsrc/devel/R-tcltk2: Makefile
Log Message:
R-tcltk2: mark as BROKEN
Infinite loop during build, see PR pkg/56696.
To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.4.12.1 pkgsrc/devel/R-tcltk2/Makefile
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
From: "Tobias Nygren" <tnn@netbsd.org>
To: gnats-bugs@gnats.NetBSD.org
Cc:
Subject: PR/56696 CVS commit: pkgsrc/devel/R-tcltk2
Date: Sat, 18 Jun 2022 09:07:37 +0000
Module Name: pkgsrc
Committed By: tnn
Date: Sat Jun 18 09:07:37 UTC 2022
Modified Files:
pkgsrc/devel/R-tcltk2: Makefile
Log Message:
R-tcltk2: PR pkg/56696: conditionally set PKG_FAIL_REASON instead of BROKEN
Reports on IRC that the package does not infinite loop if $DISPLAY is set.
To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/devel/R-tcltk2/Makefile
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
From: "Dr. Thomas Orgis" <thomas.orgis@uni-hamburg.de>
To: <gnats-bugs@NetBSD.org>
Cc:
Subject: Re: pkg/56696
Date: Sat, 18 Jun 2022 15:14:31 +0200
Some more detail: This happens when X11 is not accessible. Empty
DISPLAY is enough. Demonstrator:
# Bad.
$ mkdir -p /dev/shm/R; DISPLAY=3D LANG=3DC R --no-save --no-restore <<< 'in=
stall.packages("tcltk2", repos=3D"http://cran.ch.r-project.org", dependenci=
es=3DTRUE, lib=3D"/dev/shm/R")'
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-debian-linux-gnu (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.
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.
> install.packages("tcltk2", repos=3D"http://cran.ch.r-project.org", depend=
encies=3DTRUE, lib=3D"/dev/shm/R")
trying URL 'http://cran.ch.r-project.org/src/contrib/tcltk2_1.2-11.tar.gz'
Content type 'application/x-gzip' length 833846 bytes (814 KB)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
downloaded 814 KB
* installing *source* package 'tcltk2' ...
** package 'tcltk2' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
no DISPLAY variable so Tk is not available=20
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Terminated
[pkill R in other terminal]
# Good.
$ mkdir -p /dev/shm/R; DISPLAY=3D:0 LANG=3DC R --no-save --no-restore <<< '=
install.packages("tcltk2", repos=3D"http://cran.ch.r-project.org", dependen=
cies=3DTRUE, lib=3D"/dev/shm/R")'
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-debian-linux-gnu (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.
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.
> install.packages("tcltk2", repos=3D"http://cran.ch.r-project.org", depend=
encies=3DTRUE, lib=3D"/dev/shm/R")
trying URL 'http://cran.ch.r-project.org/src/contrib/tcltk2_1.2-11.tar.gz'
Content type 'application/x-gzip' length 833846 bytes (814 KB)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
downloaded 814 KB
* installing *source* package 'tcltk2' ...
** package 'tcltk2' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation pa=
th
* DONE (tcltk2)
The downloaded source packages are in
'/tmp/Rtmp02UZg8/downloaded_packages'
>=20
I have to wonder if the current value of DISPLAY should leak into
pkgsrc builds at all.
--=20
Dr. Thomas Orgis
HPC @ Universit=C3=A4t Hamburg
From: "Dr. Thomas Orgis" <thomas.orgis@uni-hamburg.de>
To: <gnats-bugs@NetBSD.org>
Cc:
Subject: Re: pkg/56696
Date: Sat, 18 Jun 2022 16:22:04 +0200
More debugging, on an affected system, this helps:
$ LD_PRELOAD=3D/sw/env/gcc-9.2.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libtk86.so=
:/sw/env/gcc-9.2.0_openmpi-4.0.2/pkgsrc/2019Q4/lib/libtcl86.so ~/bin/test-R=
-tcltk2
In other words: Our current tcl/tk build is to blame. This is no bug in
the R package. This is using the same compiler, the same base system
libraries. X11 from pkgsrc.
--=20
Dr. Thomas Orgis
HPC @ Universit=C3=A4t Hamburg
From: "Dr. Thomas Orgis" <thomas.orgis@uni-hamburg.de>
To: <gnats-bugs@NetBSD.org>
Cc:
Subject: Re: pkg/56696
Date: Sat, 18 Jun 2022 17:58:16 +0200
Furthermore: Downgrading lang/tcl to 8.6.9 (state from 2019Q4) and
building it in the new environment fixes this issue. So something in
tcl 8.6.12 or in our patches to it breaks things.
--=20
Dr. Thomas Orgis
HPC @ Universit=C3=A4t Hamburg
From: "Dr. Thomas Orgis" <thomas.orgis@uni-hamburg.de>
To: <gnats-bugs@NetBSD.org>
Cc:
Subject: Re: pkg/56696
Date: Mon, 20 Jun 2022 09:37:43 +0200
Am Sat, 18 Jun 2022 17:58:16 +0200
schrieb "Dr. Thomas Orgis" <thomas.orgis@uni-hamburg.de>:=20
> Furthermore: Downgrading lang/tcl to 8.6.9 (state from 2019Q4) and
> building it in the new environment fixes this issue. So something in
> tcl 8.6.12 or in our patches to it breaks things.
I tested with vanilla 8.6.12 and with various subsets of the pkgsrc
patches. It's patch-unix_Makefile.in. It changes the installation so
that these files go away
Only in tcl8.6.12-inst.orig/include: tclTomMath.h
Only in tcl8.6.12-inst.orig/include: tclTomMathDecls.h
Only in tcl8.6.12-inst.orig/lib/tcl8/8.4/platform: shell-1.1.4.tm
Only in tcl8.6.12-inst.orig/lib/tcl8/8.4: platform-1.0.18.tm
Only in tcl8.6.12-inst.orig/lib/tcl8/8.5: msgcat-1.6.1.tm
Only in tcl8.6.12-inst.orig/lib/tcl8/8.5: tcltest-2.5.3.tm
Only in tcl8.6.12-inst.orig/lib/tcl8/8.6: http-2.9.5.tm
and are replaced by these directories
Only in tcl8.6.12-inst.patched/lib/tcl8.6: http
Only in tcl8.6.12-inst.patched/lib/tcl8.6: msgcat1.6
Only in tcl8.6.12-inst.patched/lib/tcl8.6: platform1.0
Only in tcl8.6.12-inst.patched/lib/tcl8.6: shell1.1
Only in tcl8.6.12-inst.patched/lib/tcl8.6: tcltest2.5
The binaries are identical. When I create a merged install where all
these files/dirs are present, removing msgcat-1.6.1.tm is the killer to
break R-tcltk2 install without X11.
I am puzzled as to why we change the installation structure of these
modules, anyway.
--=20
Dr. Thomas Orgis
HPC @ Universit=C3=A4t Hamburg
>Unformatted:
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