NetBSD Problem Report #56696

From mlelstv@arnold.localdomain  Sun Feb  6 23:59:39 2022
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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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