Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Charles Plessy]

Hi Dirk and Aaron,

quick followup.

Le Sun, Jul 10, 2016 at 03:02:44PM +0900, Charles Plessy a écrit :
> 
> after reading the whole discussion, and looking at the history of the xvfb
> package, I opened , where I ask to change the
> Recommends relationship on xauth to a Depends.  That would prevent further
> build failures.

The xvfb maintainers refused to Depend on xauth.

> The failure happened on the hppa architecture, which is not a release
> architecture.  In addition, other hppa buildds are clean, and whithin a day,
> r-cran-rngtools was built successfully on "physik".  This also means that one
> can ask the hppa porters to clean the "bell" buildd (where the failure
> happened), since the presence of xvfb there does not seem to be necessary.

The hppa porters promptly removed xvfb from their buildd.

> If none of this works and failures pop up on release architectures, then
> I think that adding an ad-hoc test in r-cran.mk would be safe, although it
> is not the most satisfying solution.

As of now, we are sure that build will fail again of one installs xvfb without
xauth, but we also know that this happens very rarely.

Obviously, it is up to Dirk to add a test for xauth or just close the bug.

Have a nice Sunday,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Charles Plessy]

Le Thu, Jul 07, 2016 at 05:51:49PM -0500, Dirk Eddelbuettel a écrit :
> 
> What we have works. Making a change risks having to pick up pieces of
> shrapnel. I don't really have time for that --- I cannot test for every
> random piece of software being present.
> 
> But the error was in another package which I do not maintain, so I kindly ask
> you to either reassign this report, or open a new one.
> 
> I do not see this as a 'fail' in r-cran.mk.

Hi Dirk and Aaron,

after reading the whole discussion, and looking at the history of the xvfb
package, I opened , where I ask to change the
Recommends relationship on xauth to a Depends.  That would prevent further
build failures.

The failure happened on the hppa architecture, which is not a release
architecture.  In addition, other hppa buildds are clean, and whithin a day,
r-cran-rngtools was built successfully on "physik".  This also means that one
can ask the hppa porters to clean the "bell" buildd (where the failure
happened), since the presence of xvfb there does not seem to be necessary.

If none of this works and failures pop up on release architectures, then
I think that adding an ad-hoc test in r-cran.mk would be safe, although it
is not the most satisfying solution.

Have a nice Sunday,

Charles

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

On 7 July 2016 at 19:53, Aaron M. Ucko wrote:
| Dirk Eddelbuettel  writes:
| 
| > What we have works. Making a change risks having to pick up pieces of
| > shrapnel. I don't really have time for that --- I cannot test for every
| > random piece of software being present.
| 
| I see your point, but am simply asking for more robust handling of one
| specific corner case that turned out to be broken.  Adding that one
| check would have no effect in any other cases.  Would you rather require
| that every single r-* package either build-depend on xauth or
| build-conflict on xvfb?

Think this through: at the extreme you are asking me to reimplement the
package management system by avoiding one of over 20k packages. That makes no
sense.

Most r-cran-* package do not use either:

edd@max:~/src/debian/CRAN$ ls -l */debian/control | wc -l
134
edd@max:~/src/debian/CRAN$ grep xauth */debian/control | wc -l
21
edd@max:~/src/debian/CRAN$

(Counts approximate as I may have two versions of a package, but I recently
trimmed the directory so that may be a handful at most and can be ignored
here.) 

This could have happened to any one of these 134 - 21 = 113.  But generally
it doesn't.

I really think we should close this, and I plan to.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Aaron M. Ucko]

Dirk Eddelbuettel  writes:

> What we have works. Making a change risks having to pick up pieces of
> shrapnel. I don't really have time for that --- I cannot test for every
> random piece of software being present.

I see your point, but am simply asking for more robust handling of one
specific corner case that turned out to be broken.  Adding that one
check would have no effect in any other cases.  Would you rather require
that every single r-* package either build-depend on xauth or
build-conflict on xvfb?

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

On 7 July 2016 at 18:45, Aaron M. Ucko wrote:
| Dirk Eddelbuettel  writes:
| 
| > We had r-cran.mk as is for a few (ten) thousand builds by now. It works. 
Here
| > either r-cran-rngtools or the autobuilder seems to be at fault.
| 
| r-cran-rngtools had the misfortune to encounter an autobuilder that
| supplied a non-minimal environment it (via r-cran.mk) wasn't prepared to
| handle, and would not normally encounter in practice.  I agree that the
| autobuilder should have supplied a minimal environment, which would have
| worked fine.  All the same, the environment it did supply was technically
| legal, so r-cran.mk should have accommodated it -- especially since doing
| so would just require a simple one-line change.

What we have works. Making a change risks having to pick up pieces of
shrapnel. I don't really have time for that --- I cannot test for every
random piece of software being present.

But the error was in another package which I do not maintain, so I kindly ask
you to either reassign this report, or open a new one.

I do not see this as a 'fail' in r-cran.mk.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Aaron M. Ucko]

Dirk Eddelbuettel  writes:

> We had r-cran.mk as is for a few (ten) thousand builds by now. It works. Here
> either r-cran-rngtools or the autobuilder seems to be at fault.

r-cran-rngtools had the misfortune to encounter an autobuilder that
supplied a non-minimal environment it (via r-cran.mk) wasn't prepared to
handle, and would not normally encounter in practice.  I agree that the
autobuilder should have supplied a minimal environment, which would have
worked fine.  All the same, the environment it did supply was technically
legal, so r-cran.mk should have accommodated it -- especially since doing
so would just require a simple one-line change.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

On 7 July 2016 at 16:04, Aaron M. Ucko wrote:
| Dirk Eddelbuettel  writes:
| 
| > Our default build does not use xvfb-run, we only this 'as needed' and eg in
| > all of my packages that have xvfb I *also* have xauth:
| 
| Right, and that's as it should be.  r-cran-rngtools build-depends on
| neither, which is also perfectly reasonable.  However, one particular
| build of r-cran-rngtools somehow wound up running in a non-minimal, but
| technically legal, build environment that threw r-cran.mk off.  Whoever
| maintains that autobuilder might want to look into cleaning it up, but
| meanwhile, r-cran.mk should cope with whatever it finds.

I am not sure I agree.

We had r-cran.mk as is for a few (ten) thousand builds by now. It works. Here
either r-cran-rngtools or the autobuilder seems to be at fault.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Aaron M. Ucko]

Dirk Eddelbuettel  writes:

> Our default build does not use xvfb-run, we only this 'as needed' and eg in
> all of my packages that have xvfb I *also* have xauth:

Right, and that's as it should be.  r-cran-rngtools build-depends on
neither, which is also perfectly reasonable.  However, one particular
build of r-cran-rngtools somehow wound up running in a non-minimal, but
technically legal, build environment that threw r-cran.mk off.  Whoever
maintains that autobuilder might want to look into cleaning it up, but
meanwhile, r-cran.mk should cope with whatever it finds.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

On 7 July 2016 at 14:18, Dirk Eddelbuettel wrote:
| 
| On 7 July 2016 at 14:59, Aaron M. Ucko wrote:
| | Dirk Eddelbuettel  writes:
| | 
| | > A Depends: added to r-base-dev, which all packages Build-Depends: on, 
should
| | > do this, right?
| | 
| | Yes, that would also work.
| 
| Turns out that xvfb is not in there so maybe I go back to checking in
| r-cran.mk as first suggested.

Or maybe r-cran-rngtools needs to Build-Depends: on xauth?

Our default build does not use xvfb-run, we only this 'as needed' and eg in
all of my packages that have xvfb I *also* have xauth:

edd@max:~/src/debian/CRAN$ grep xvfb */debian/control
cairoDevice-2.23/debian/control:Build-Depends: debhelper (>= 7.0.0), cdbs,
r-base-dev (>= 3.3.1), libgtk2.0-dev, libcairo2-dev, xvfb, xauth, xfonts-base
fAsianOptions-3010.79/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.1), cdbs, r-cran-fbasics (>= 2160.81-2), r-cran-foptions
(>= 270.74), xvfb, xauth, xfonts-base
fAssets-3011.83/debian/control:Build-Depends: debhelper (>= 7), r-base-dev
(>= 3.3.1), cdbs, r-cran-sn, r-cran-mass, r-cran-robustbase, r-cran-timedate,
r-cran-timeseries, r-cran-fbasics (>= 290.76), r-cran-fmul\
tivar, xvfb, xauth, xfonts-base, r-cran-ecodist, r-cran-mvnormtest,
r-cran-energy
fBasics-3011.87/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.2.0), cdbs, r-cran-mass, r-cran-timedate, r-cran-timeseries
(>= 2100.84), r-cran-stabledist, xvfb, xauth, xfonts-base, r-cran-\
gss
fBonds-3010.77/debian/control:Build-Depends: debhelper (>= 7.0.0), r-base-dev
(>= 3.0.2), cdbs, r-cran-fbasics (>= 290.76), xvfb, xauth, xfonts-base
fCopulae-3011.81/debian/control:Build-Depends: debhelper (>= 7), r-base-dev
(>= 3.3.0), cdbs, r-cran-sn, r-cran-timedate, r-cran-timeseries,
r-cran-fbasics (>= 2100.78), r-cran-fmultivar, xvfb, xauth, xfonts-bas\
e
fExoticOptions-2152.78/debian/control:Build-Depends: debhelper, r-base-dev
(>= 3.0.0~), cdbs, r-cran-fbasics (>= 290.76), r-cran-foptions (>= 260.72),
xvfb, xauth, xfonts-base
fExtremes-3010.81/debian/control:Build-Depends: debhelper, r-base-dev (>=
3.3.1), cdbs, r-cran-timedate, r-cran-timeseries, r-cran-fbasics (>= 290.76),
r-cran-fgarch, r-cran-ftrading, xvfb, xauth, xfonts-base
fGarch-3010.82/debian/control:Build-Depends: debhelper (>= 7.0.0), r-base-dev
(>= 3.3.1), cdbs, r-cran-fbasics (>= 2100.78), r-cran-timedate,
r-cran-timeseries, r-cran-vr, xvfb, xauth, xfonts-base
fImport-3000.82/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.1), cdbs, r-cran-timeseries, xvfb, xauth, xfonts-base
fMultivar-3011.78/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.1), cdbs, r-cran-fbasics (>= 290.76), r-cran-sn, xvfb,
xauth, xfonts-base, r-cran-mvtnorm, r-cran-cubature
fNonlinear-3010.78/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.0), cdbs, r-cran-fbasics (>= 2100.78), r-cran-fgarch (>=
2100.79), xvfb, xauth, xfonts-base
fOptions-3022.85/debian/control:Build-Depends: debhelper (>= 7), r-base-dev
(>= 3.2.2), cdbs, r-cran-fbasics (>= 290.76), xvfb, xauth, xfonts-base
fPortfolio-3011.81/debian/control:Build-Depends: debhelper, r-base-dev (>=
3.3.1), cdbs, r-cran-mass, r-cran-timedate, r-cran-timeseries,
r-cran-fbasics, r-cran-fassets (>= 2100.78), r-cran-quadprog, r-cran-rglp\
k, r-cran-rneos, r-cran-fcopulae, r-cran-rsymphony, r-cran-rsolnp,
r-cran-kernlab, xvfb, xauth, xfonts-base
fRegression-3011.81/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.1), cdbs, r-cran-mgcv, r-cran-vr, r-cran-polspline,
r-cran-fbasics (>= 290.76), r-cran-ftrading, r-cran-fmultivar, r-cra\
n-nnet, r-cran-lmtest, xvfb, xauth, xfonts-base
fTrading-3010.78/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.3.1), cdbs, r-cran-fbasics (>= 290.76), xvfb, xauth,
xfonts-base
fUnitRoots-3010.78/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.0.1), cdbs, r-cran-fbasics (>= 260.72), r-cran-urca (>=
1.2-5-2), xvfb, xauth, xfonts-base
relimp-1.0-5/debian/control:Build-Depends: debhelper (>= 7.0), r-base-dev (>=
3.3.1), cdbs, xvfb, xauth, xfonts-base
rggobi-2.1.20/debian/control:Build-Depends: r-base-dev (>= 3.1.0), ggobi (>=
2.1.6), debhelper (>= 7.0.0), cdbs, libgtk2.0-dev, libxml2-dev, r-cran-rgtk2,
xvfb, xauth, xfonts-base
Rmetrics-2100.77/debian/control:Build-Depends: debhelper (>= 5.0.0),
r-base-dev (>= 2.10.0), cdbs, r-cran-fecofin, r-cran-futilities,
r-cran-timedate, r-cran-timeseries, r-cran-fimport, r-cran-fbasics,
r-cran-fa\
rma, r-cran-fgarch, r-cran-fnonlinear, r-cran-funitroots, r-cran-ftrading,
r-cran-fmultivar, r-cran-fregression, r-cran-fextremes, r-cran-fcopulae,
r-cran-foptions, r-cran-fexoticoptions, r-cran-fasianoptions, r\
-cran-fassets, r-cran-fportfolio, xvfb, xbase-clients, xfonts-base
timeDate-3012.100/debian/control:Build-Depends: debhelper (>= 7.0.0),
r-base-dev (>= 3.1.2), cdbs, xvfb, xauth, xfonts-base
timeSeries-3022.101.2/debian/control:Build-Depends: 

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

On 7 July 2016 at 14:59, Aaron M. Ucko wrote:
| Dirk Eddelbuettel  writes:
| 
| > A Depends: added to r-base-dev, which all packages Build-Depends: on, should
| > do this, right?
| 
| Yes, that would also work.

Turns out that xvfb is not in there so maybe I go back to checking in
r-cran.mk as first suggested.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Aaron M. Ucko]

Dirk Eddelbuettel  writes:

> A Depends: added to r-base-dev, which all packages Build-Depends: on, should
> do this, right?

Yes, that would also work.

Thanks!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Dirk Eddelbuettel]

Hi Aaron,

On 7 July 2016 at 14:09, Aaron M. Ucko wrote:
| Package: r-base-dev
| Version: 3.3.1-1
| Severity: normal
| 
| When determening whether to run tests directly or under xvfb-run,
| r-cran.mk should check for the presence of both xvfb-run and xauth.
| As it is, the hppa build of r-cran-rngtools somehow wound up running
| in an environment with xvfb but not xauth (which xvfb merely
| recommends) and failing:
| 
|   if test -f /usr/bin/xvfb-run; then  \
|xvfb-run -a\
|   R CMD INSTALL -l 
/<>/debian/r-cran-rngtools/usr/lib/R/site-library --clean \
|.  \
|   "--built-timestamp=\"Sun, 03 Jul 2016 22:30:22 
+0200\"" \
|   ;   \
|   else\
|R CMD INSTALL -l 
/<>/debian/r-cran-rngtools/usr/lib/R/site-library\
|   --clean  .  \
|   "--built-timestamp=\"Sun, 03 Jul 2016 22:30:22 
+0200\"" \
|   ;   \
|   fi
|   xvfb-run: error: xauth command not found
|   /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
|   make: *** [R_any_arch] Error 3
|   dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit 
status 2

Interesting.

A Depends: added to r-base-dev, which all packages Build-Depends: on, should
do this, right?

Dirk
 
| 
https://buildd.debian.org/status/fetch.php?pkg=r-cran-rngtools=hppa=1.2.4-1=1467911686
| 
| -- System Information:
| Debian Release: stretch/sid
|   APT prefers testing
|   APT policy: (500, 'testing'), (500, 'stable'), (300, 'unstable')
| Architecture: amd64 (x86_64)
| Foreign Architectures: i386
| 
| Kernel: Linux 4.6.0-1-amd64 (SMP w/4 CPU cores)
| Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
| Shell: /bin/sh linked to /bin/dash
| Init: systemd (via /run/systemd/system)
| 
| Versions of packages r-base-dev depends on:
| ii  build-essential11.7
| ii  cdbs   0.4.142
| ii  g++4:5.3.1-3
| ii  gcc4:5.3.1-3
| ii  gfortran   4:5.3.1-3
| ii  libatlas-base-dev  3.10.2-9+b1
| ii  libblas-dev3.6.1-1
| ii  libbz2-dev 1.0.6-8
| ii  libicu-dev 55.1-7
| ii  libjpeg62-turbo-dev [libjpeg-dev]  1:1.5.0-1
| ii  liblapack-dev  3.6.1-1
| ii  liblzma-dev5.1.1alpha+20120614-2.1
| ii  libncurses5-dev6.0+20160319-2+b1
| ii  libpcre3-dev   2:8.38-3.1
| ii  libpng-dev 1.6.23-1
| ii  libreadline-dev6.3-8+b4
| ii  r-base-core3.3.1-1
| ii  zlib1g-dev 1:1.2.8.dfsg-2+b1
| 
| r-base-dev recommends no packages.
| 
| Versions of packages r-base-dev suggests:
| ii  debhelper9.20160403
| ii  texinfo  6.1.0.dfsg.1-8
| ii  texlive-base 2016.20160623-1
| ii  texlive-extra-utils  2016.20160623-1
| ii  texlive-fonts-extra  2016.20160623-1
| ii  texlive-fonts-recommended2016.20160623-1
| ii  texlive-generic-recommended  2016.20160623-1
| ii  texlive-latex-base   2016.20160623-1
| ii  texlive-latex-extra  2016.20160623-1
| ii  texlive-latex-recommended2016.20160623-1
| 
| -- no debconf information

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Bug#830266: r-base-dev: r-cran.mk should check for xauth, not just xvfb-run

[Aaron M. Ucko]

Package: r-base-dev
Version: 3.3.1-1
Severity: normal

When determening whether to run tests directly or under xvfb-run,
r-cran.mk should check for the presence of both xvfb-run and xauth.
As it is, the hppa build of r-cran-rngtools somehow wound up running
in an environment with xvfb but not xauth (which xvfb merely
recommends) and failing:

  if test -f /usr/bin/xvfb-run; then\
 xvfb-run -a\
R CMD INSTALL -l 
/<>/debian/r-cran-rngtools/usr/lib/R/site-library --clean \
 .  \
"--built-timestamp=\"Sun, 03 Jul 2016 22:30:22 
+0200\"" \
;   \
else\
 R CMD INSTALL -l 
/<>/debian/r-cran-rngtools/usr/lib/R/site-library\
--clean  .  \
"--built-timestamp=\"Sun, 03 Jul 2016 22:30:22 
+0200\"" \
;   \
fi
  xvfb-run: error: xauth command not found
  /usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch' failed
  make: *** [R_any_arch] Error 3
  dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit 
status 2

https://buildd.debian.org/status/fetch.php?pkg=r-cran-rngtools=hppa=1.2.4-1=1467911686

-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (500, 'testing'), (500, 'stable'), (300, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.6.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages r-base-dev depends on:
ii  build-essential11.7
ii  cdbs   0.4.142
ii  g++4:5.3.1-3
ii  gcc4:5.3.1-3
ii  gfortran   4:5.3.1-3
ii  libatlas-base-dev  3.10.2-9+b1
ii  libblas-dev3.6.1-1
ii  libbz2-dev 1.0.6-8
ii  libicu-dev 55.1-7
ii  libjpeg62-turbo-dev [libjpeg-dev]  1:1.5.0-1
ii  liblapack-dev  3.6.1-1
ii  liblzma-dev5.1.1alpha+20120614-2.1
ii  libncurses5-dev6.0+20160319-2+b1
ii  libpcre3-dev   2:8.38-3.1
ii  libpng-dev 1.6.23-1
ii  libreadline-dev6.3-8+b4
ii  r-base-core3.3.1-1
ii  zlib1g-dev 1:1.2.8.dfsg-2+b1

r-base-dev recommends no packages.

Versions of packages r-base-dev suggests:
ii  debhelper9.20160403
ii  texinfo  6.1.0.dfsg.1-8
ii  texlive-base 2016.20160623-1
ii  texlive-extra-utils  2016.20160623-1
ii  texlive-fonts-extra  2016.20160623-1
ii  texlive-fonts-recommended2016.20160623-1
ii  texlive-generic-recommended  2016.20160623-1
ii  texlive-latex-base   2016.20160623-1
ii  texlive-latex-extra  2016.20160623-1
ii  texlive-latex-recommended2016.20160623-1

-- no debconf information