[Debian-med-packaging] Bug#845753: Possible workaround

Wed Dec 14 21:57:13 UTC 2016

On 14 December 2016 at 16:44, Christian Seiler wrote:
| Hi,
| 
| On 12/14/2016 04:16 PM, Dirk Eddelbuettel wrote:
| > One quick thought: does it die in _compilation_ which we have seen with other
| > (C++-heavy) packages?
| 
| No, g++ works fine here. (The C++ file itself is trivial if you
| look at it.)
| 
| Current package in Debian:
| http://sources.debian.net/src/r-cran-treescape/1.10.18-2/
| 
| > Otherwise if it fails _after_ compilation we may be able to get by turning
| > some default aspects of R CMD INSTALL off:
| > 
| >       --no-byte-compile do not byte-compile R code
| 
| That doesn't help, still fails. :-(
| 
| >       --no-test-load    skip test of loading installed package
| 
| That doesn't help either. :-(
| 
| >From the build log when it fails (8 MiB stack limit):
| 
| * installing *source* package 'treescape' ...
| ** package 'treescape' successfully unpacked and MD5 sums checked
| ** libs
| g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CPP_update_combinations.cpp -o CPP_update_combinations.o
| g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
| g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o treescape.so CPP_update_combinations.o RcppExports.o -L/usr/lib/R/lib -lR
| installing to /home/christian/r-cran-treescape-1.10.18/debian/r-cran-treescape/usr/lib/R/site-library/treescape/libs
| ** R
| ** data
| *** moving datasets to lazyload DB
| ** inst
| ** preparing package for lazy loading
| Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
| Warning in rgl.init(initValue, onlyNULL) :
|   RGL: unable to open X11 display
| Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
| Error: segfault from C stack overflow
| * removing '/home/christian/r-cran-treescape-1.10.18/debian/r-cran-treescape/usr/lib/R/site-library/treescape'
| 
| (Ignore the X warnings, they are irrelevant here, I'm too lazy to run
| it in xvfb and it's in a VM without X.)

xvfb does not given you OpenGL. This wants X11 _and OpenGL_.

Because of that, I think it would be worthwhile to check if it were to build
without the need for rgl.

Else the '--no-test-load' added to the 'R CMD INSTALL' call should skip all
that.  We would need a local copy of r-cran.mk, or just copy it and adjust.

Maybe Andreas can give you a hand?

| When it succeeds (195.3 MiB stack limit):
| 
| * installing *source* package 'treescape' ...
| ** package 'treescape' successfully unpacked and MD5 sums checked
| ** libs
| g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CPP_update_combinations.cpp -o CPP_update_combinations.o
| g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
| g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o treescape.so CPP_update_combinations.o RcppExports.o -L/usr/lib/R/lib -lR
| installing to /home/christian/r-cran-treescape-1.10.18/debian/r-cran-treescape/usr/lib/R/site-library/treescape/libs
| ** R
| ** data
| *** moving datasets to lazyload DB
| ** inst
| ** preparing package for lazy loading
| Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
| Warning in rgl.init(initValue, onlyNULL) :
|   RGL: unable to open X11 display
| Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
| ** help
| *** installing help indices
| ** building package indices
| ** installing vignettes
| ** testing if installed package can be loaded
| Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
| Warning in rgl.init(initValue, onlyNULL) :
|   RGL: unable to open X11 display
| Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
| * DONE (treescape)
| 
| So the problem occurs at the following step:
| 
|   ** preparing package for lazy loading
| 
| And, to recap the specific circumstances where this problem appears:
| 
|  - 32bit
|  - Little Endian architecture
|  - Linux 3.16
|  - Standard stack size limit (8 MiB)
|  - treescape module version >= 1.10.17
| 
| Change only one of these things and it will work:
| 
|  - 64bit Little Endian Linux 3.16, standard stack limit: works
|       e.g. amd64, arm64
|  - 32bit Big Endian Linux 3.16, standard stack limit: works
|       e.g. powerpc
|  - 32bit Little Endian Linux 4.7.x or higher, standard stack limit: works
|       e.g. i386 on my own system with newer kernel, or the mipsel
|       build server of Debian with a backported kernel
|  - 32bit Little Endian Linux 3.16, huge stack limit: works
|  - older version 1.9.18: works
| 
| Note that different kernel versions really mean just the kernel,
| the libraries and tools are 100% identical. (I mean libc, R, gcc,
| and so on.)
| 
| I'm at a complete loss why the kernel version is even relevant here
| btw., since the program uses a huge stack, but there is no system
| call related stuff going on (and the package doesn't appear to
| interface directly with the kernel anyway, it's much too high level
| for that), and the problem persists for the given kernel over a lot
| of very different architectures.

It sounds like a bug at the system level. R packages tend not to be that
greedy at build or load.

Dirk

| gdb stack trace of the R process when the stack limit is hit can be
| found in this email of mine:
| https://lists.debian.org/debian-mentors/2016/12/msg00412.html
| (Debug symbols were installed, R version 3.3.2.)
| 
| Regards,
| Christian

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