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 | e...@debian.org
