Opened 9 years ago
Closed 8 years ago
#11970 closed defect (fixed)
r2.10.1.p4 may fail to configure with readline (BLOCKS Sage from building on Ubuntu 11.10)
Reported by:  Snark  Owned by:  tbd 

Priority:  blocker  Milestone:  sage4.8 
Component:  packages: standard  Keywords:  Oneiric Ocelot Ubuntu 11.10 ARM libtermcap libncurses libtinfo rproject sd35.5 
Cc:  zimmerma  Merged in:  sage4.8.rc0 
Authors:  Leif Leonhardy  Reviewers:  Jeroen Demeyer 
Report Upstream:  N/A  Work issues:  
Branch:  Commit:  
Dependencies:  #12282  Stopgaps: 
Description (last modified by )
I was having a hard time compiling sage on my ARM box : the R spkg, which until then hadn't given any issue, didn't even want to configure.
The reason was that if ncurses is detected, then termcap isn't searched for, and hence detecting rl_callback_read_char fails (missing ltermacp means missing symbols) ; which means the configuration failed because withreadline was given on the commandline, and it wasn't correctly detected.
I got around it by uninstalling the libncurses5dev package from my system.
Looking at the configure.ac, I think the issue isn't ARMspecific ; perhaps that should be pushed upstream.
New spkg:
Attachments (2)
Change History (52)
comment:1 Changed 9 years ago by
 Keywords Oneiric Ocelot Ubuntu 11.10 ARM libtermcap libncurses libtinfo added
 Summary changed from r2.10.1.p4 doesn't configure is ncurse is found to r2.10.1.p4 may fail to configure with readline
comment:2 Changed 9 years ago by
 Component changed from build to packages
 Owner changed from GeorgSWeber to tbd
comment:3 Changed 9 years ago by
P.S.: You should give more details about your configuration.
On many systems, libtermcap.so
is (or used to be) just a symbolic link to libncurses.so
. On Oneiric, with libreadlinedev
installed, libncurses.so
is a linker script, which causes problems.
comment:4 Changed 9 years ago by
Btw., since Sage also ships a termcap package, we should perhaps also build a shared library of that as well, at least if the systems lacks one.
Or, if the system does have a "devel version" of libtermcap (headers, static library and an "unversioned" .so
), don't build / install Sage's at all.
comment:5 followup: ↓ 6 Changed 9 years ago by
As discussed on irc, the readline package compiled, and I'm now managing to compile R with even with the previously problematic headers installed.
comment:6 in reply to: ↑ 5 Changed 9 years ago by
Replying to Snark:
As discussed on irc, the readline package compiled, and I'm now managing to compile R with even with the previously problematic headers installed.
Fine. Michael Anselmi also reported on sagerelease:
Good news! To have sage4.7.2.rc1 build properly on Ubuntu 11.10, all I had to do was replace $SAGE_ROOT/spkg/standard/readline6.1.pkg with readline6.2.p2.spkg (the spkg you provided) before running `make'.
(Although he did get an apparently unrelated doctest error, related to LaTeX.)
I'll commit the changes, update the spkg (inplace) and update the ticket's description later.
comment:8 Changed 9 years ago by
 Keywords rproject added
 Milestone set to sage4.8
comment:9 Changed 8 years ago by
 Priority changed from major to blocker
 Summary changed from r2.10.1.p4 may fail to configure with readline to r2.10.1.p4 may fail to configure with readline (BLOCKS Sage from building on Ubuntu 11.10)
I just tried building the latest sage4.8.alpha5 on the latest Ubuntu11.10. It includes an spkg called "readline6.2.p2". Nonetheless, the build failed with:
... checking for history_truncate_file... no configure: error: withreadline=yes (default) and headers/libs are not available Error configuring R. ************************************************************************ Error installing package r2.14.0.p1 ************************************************************************
This is a different readline6.2.p2 than the one leif posted above. Installing leif's package, I was then able to build R.
I'm bumping the priority of this ticket up to BLOCKER, since we can't release Sage with it not even building on the current version of the most popular Linux distribution.
comment:10 followup: ↓ 11 Changed 8 years ago by
I used Leif's spkg above with 4.8.alpha4, and although the build finished, Sage doesn't start; I get a segfault from IPython. I'm using Ubuntu 11.10. Is anyone else seeing this?
comment:11 in reply to: ↑ 10 ; followup: ↓ 12 Changed 8 years ago by
Replying to ddrake:
I used Leif's spkg above with 4.8.alpha4, and although the build finished, Sage doesn't start; I get a segfault from IPython. I'm using Ubuntu 11.10. Is anyone else seeing this?
Dan, I saw exactly the same thing. I posted on sagedevel about this just now. I was able to get around all problems and now have a seemingly functional version of Sage running on 11.10.
comment:12 in reply to: ↑ 11 ; followup: ↓ 14 Changed 8 years ago by
Replying to was:
Dan, I saw exactly the same thing. I posted on sagedevel about this just now. I was able to get around all problems and now have a seemingly functional version of Sage running on 11.10.
Hmmm...in your message (https://groups.google.com/d/msg/sagerelease/sXdDXME5Ds4/4CpiS04wT28J) you get a segfault from some matrix code. But I don't even get a traceback. This is what I get:
drake@klee:/scratch/sage4.8.alpha4$ ./sage   Sage Version 4.8.alpha4, Release Date: 20111213   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** local/bin/sagesage: line 305: 28355 Segmentation fault sageipython "$@" i
Although I see you used alpha5, and I'm using alpha4. That might be relevant, but maybe not.
Interestingly, sage ipython
(note the space!) works fine. So my problem is somewhere in sageipython
(note no space!); something with the library flags??
comment:13 Changed 8 years ago by
The readline6.2.p2 is from #12131, I think.
Leif: Can you merge the oneline change from that readline into a .p3 and clean it up for review? Right now there are notyet checked in changes...
comment:14 in reply to: ↑ 12 ; followup: ↓ 15 Changed 8 years ago by
Replying to ddrake:
Replying to was:
Dan, I saw exactly the same thing. I posted on sagedevel about this just now. I was able to get around all problems and now have a seemingly functional version of Sage running on 11.10.
Hmmm...in your message (https://groups.google.com/d/msg/sagerelease/sXdDXME5Ds4/4CpiS04wT28J) you get a segfault from some matrix code. But I don't even get a traceback. This is what I get:
drake@klee:/scratch/sage4.8.alpha4$ ./sage   Sage Version 4.8.alpha4, Release Date: 20111213   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** local/bin/sagesage: line 305: 28355 Segmentation fault sageipython "$@" iAlthough I see you used alpha5, and I'm using alpha4. That might be relevant, but maybe not.
Interestingly,
sage ipython
(note the space!) works fine. So my problem is somewhere insageipython
(note no space!); something with the library flags??
That's the kind of output you get with the failure from matrix_modn_float if you don't start sage with "gdb" see my own follow up in that thread. alpha3,4,5 is irrelevant here. And this is not related to R or readline but #4260.
comment:15 in reply to: ↑ 14 Changed 8 years ago by
Replying to fbissey:
That's the kind of output you get with the failure from matrix_modn_float if you don't start sage with "gdb" see my own follow up in that thread. alpha3,4,5 is irrelevant here. And this is not related to R or readline but #4260.
Ah, you are right. And I can confirm that the patch you included (https://groups.google.com/d/msg/sagerelease/sXdDXME5Ds4/pteQHfW2APYJ) allows 4.8.alpha4 to start and pass all doctests in sage/matrix on my Ubuntu 11.10 machine!
comment:16 Changed 8 years ago by
These issues with segfaults on startup are being addressed at #12157.
comment:17 Changed 8 years ago by
bump Leif: Can you merge the oneline change from that readline into a .p3 (starting from #12131) and clean it up for review?
comment:18 Changed 8 years ago by
 Description modified (diff)
 Status changed from new to needs_review
I've posted an updated version of Leif's spkg, although without the changes to spkgcheck
.
comment:19 followup: ↓ 20 Changed 8 years ago by
Is this one of the blockers for 4.8 release? In which case some concerted effort to get it reviewed is surely urgent?
Using readline6.2.p2.spkg I just helped my colleague Bruce Westbury build Sage on an old laptop on which he had installed ubuntu 11.10 (which is still building) but realised later that he was building 4.7.2 and not any 4.8.alpha. The only ubuntu 11.10 machine I have is a slow netbook on which I built 4.7.2 before upgrading from ubuntu 11.04. I can try this patch out on that but it may take a few days.
comment:20 in reply to: ↑ 19 Changed 8 years ago by
Replying to cremona:
Is this one of the blockers for 4.8 release? In which case some concerted effort to get it reviewed is surely urgent?
Yes, it is. And I certainly hope this will get fixed rather quickly.
comment:21 Changed 8 years ago by
 Cc zimmerma added
 Reviewers set to Jeroen Demeyer
The spkg looks good on first sight. I can of course not test it on every system. So I'm willing to give it positive_review if somebody can confirm that it actually fixes the problem on Ubuntu 11.10. I asked Paul Zimmermann to do this.
comment:22 followups: ↓ 23 ↓ 27 Changed 8 years ago by
Bruce and I used readline6.2.p2.spkg not the p3, and also used it on a fresh build of 4.7.2 (which had previously stalled building R). So the following might not be relevant: after building, when we run Sage it gives a 2line warning that readline is not available  and indeed Sage has no history functions. What did we do wrong?
Bruce also tells me that although he installed all the ubuntu packages listed on the installation web page, he also had to install dpkgdev before Sage would build.
comment:23 in reply to: ↑ 22 Changed 8 years ago by
Replying to cremona:
Bruce and I used readline6.2.p2.spkg not the p3, and also used it on a fresh build of 4.7.2 (which had previously stalled building R). So the following might not be relevant: after building, when we run Sage it gives a 2line warning that readline is not available  and indeed Sage has no history functions. What did we do wrong?
I got the same thing using the "p3" spkg. But the build finished and (I think) passed tests.
comment:24 Changed 8 years ago by
I also tried the p3 spkg, and indeed the build finished, but:
tiramisu% ./sage   Sage Version 4.8.alpha5, Release Date: 20111221   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** WARNING: Readline services not available on this platform. WARNING: The autoindent feature requires the readline library
However I only applied the spkg, not the patch.
Paul
comment:25 followups: ↓ 28 ↓ 35 Changed 8 years ago by
On sage.math with:
 the new readline spkg from this ticket
 compiled with gcc4.2.4
 #12263 applied
the following happens (and all 3 conditions above are needed):
$ ./sage c True mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libcsage.so(print_backtrace+0x2b)[0x7f22311cd3a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libcsage.so(sigdie+0x14)[0x7f22311cd3ce] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libcsage.so(sage_signal_handler+0x201)[0x7f22311cd031] /lib/libpthread.so.0[0x7f2232dd37d0] /lib/libc.so.6(strcmp+0x2)[0x7f2232455b42] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(tgetent+0xc4)[0x7f222bb2d18c] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(_rl_init_terminal_io+0x306)[0x7f222bb24fc6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(rl_initialize+0x87)[0x7f222bb0f5b7] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/python2.6/libdynload/readline.so(initreadline+0x15f)[0x7f222bd4248f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(_PyImport_LoadDynamicModule+0xc2)[0x7f22330ddc42] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbfb2] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x12a)[0x7f22330dc1ca] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x169)[0x7f22330dc209] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x169)[0x7f22330dc209] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x12a)[0x7f22330dc1ca] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x6452)[0x7f22330c3552] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dd018] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbfb2] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x12a)[0x7f22330dc1ca] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x12a)[0x7f22330dc1ca] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x12a)[0x7f22330dc1ca] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x169)[0x7f22330dc209] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ExecCodeModuleEx+0xc2)[0x7f22330d8b52] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330db368] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dba59] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330dbf2b] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyImport_ImportModuleLevel+0x169)[0x7f22330dc209] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0[0x7f22330bbdcd] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyObject_Call+0x68)[0x7f2233026f48] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_CallObjectWithKeywords+0x56)[0x7f22330bc4f6] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x214f)[0x7f22330bf24f] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x891)[0x7f22330c49a1] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f22330c4a72] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0xc1)[0x7f22330e8871] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(PyRun_SimpleFileExFlags+0x1f9)[0x7f22330e8b49] /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libpython2.6.so.1.0(Py_Main+0xa71)[0x7f22330f4591] /lib/libc.so.6(__libc_start_main+0xf4)[0x7f22323f91c4] python[0x400679]  Unhandled SIGSEGV: A segmentation fault occurred in Sage. This probably occurred because a *compiled* component of Sage has a bug in it and is not properly wrapped with sig_on(), sig_off(). You might want to run Sage under gdb with 'sage gdb' to debug this. Sage will now terminate.  local/bin/sagesage: line 766: 23516 Segmentation fault sageeval "$@"
comment:26 Changed 8 years ago by
 Status changed from needs_review to needs_work
comment:27 in reply to: ↑ 22 Changed 8 years ago by
Replying to cremona:
Bruce and I used readline6.2.p2.spkg not the p3, and also used it on a fresh build of 4.7.2 (which had previously stalled building R). So the following might not be relevant: after building, when we run Sage it gives a 2line warning that readline is not available  and indeed Sage has no history functions. What did we do wrong?
Before building Sage (or [re]installing Sage's readline), you need to
$ sudo aptget install libncurses5dev libncursesw5dev
(The latter depends on the former, so you actually have to specify only one of them). You do not have to install any libreadline package, as Sage builds and uses its own  the one we're talking about here.
Bruce also tells me that although he installed all the ubuntu packages listed on the installation web page, he also had to install dpkgdev before Sage would build.
I'm pretty sure the instructions on the web page are still outdated (and by the way have been wrong anyway), as discussed with Harald on sagerelease a while ago.
dpkgdev
is needed since Ubuntu 11.04, in order to make Python build (because the locations of some libraries were changed in Debian/Ubuntu?).
I'm sorry I'm unable to work much on Sage at the moment; thanks John for providing an updated and rebased spkg of my preliminary one.
comment:28 in reply to: ↑ 25 Changed 8 years ago by
Replying to jdemeyer:
On sage.math with:
 the new readline spkg from this ticket
 compiled with gcc4.2.4
 #12263 applied
the following happens (and all 3 conditions above are needed):
... > /lib/libc.so.6(strcmp+0x2)[0x7f2232455b42] > /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(tgetent+0xc4)[0x7f222bb2d18c] > /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(_rl_init_terminal_io+0x306)[0x7f222bb24fc6] > /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/libreadline.so.6(rl_initialize+0x87)[0x7f222bb0f5b7] > /mnt/usb1/scratch/jdemeyer/merger/sage4.8.rc1/local/lib/python2.6/libdynload/readline.so(initreadline+0x15f)[0x7f222bd4248f] ...
Can you track this further down?
I tried tgetent(NULL, NULL)
on sage.math
(with GCC 4.2.4), which doesn't segfault but properly returns 1. Could you try setting TERM
to something else (rather than unsetting it) in sagesage
, as suggested at #12263?
comment:29 followup: ↓ 33 Changed 8 years ago by
Here is a first interesting data point:
Let tgetent_test.c
be following file:
#include <termcap.h> #include <stdlib.h> int main(int argc, char** argv) { char* buf = malloc(100000); tgetent(buf, "dumb"); }
Compiling this with
$ gcc ltermcap tgetent_test.c o tgetent_test
and running it works flawlessly.
However, the same gcc command with the Sage environment variables gives
$ ( source local/bin/sageenv; gcc ltermcap tgetent_test.c o tgetent_test ) /tmp/ccwDi3Oi.o: In function `main': tgetent_test.c:(.text+0x27): undefined reference to `tgetent' collect2: ld returned 1 exit status
With gcc4.5.1 (which I happen to have installed in my own $HOME directory), the compilation works fine again.
comment:30 Changed 8 years ago by
Deleting the file $SAGE_ROOT/local/lib/libtermcap.a
solves the problem. Somehow that staticonly library confuses the linker. Not sure whether this is a linker bug or feature.
comment:31 Changed 8 years ago by
Note: the output of readline6.2.p3.log
is exactly the same whether or not local/lib/libtermcap.a
exists. From my observations above, I would expect the readline build to fail when local/bin/libtermcap.a
exists. But it doesn't, so maybe it finds a broken tgetent()
somewhere somehow.
comment:32 Changed 8 years ago by
That's it for now, going to sleep...
comment:33 in reply to: ↑ 29 Changed 8 years ago by
Replying to jdemeyer:
Here is a first interesting data point:
Let
tgetent_test.c
be following file:
#include <termcap.h> #include <stdlib.h> int main(int argc, char** argv) { char* buf = malloc(100000); tgetent(buf, "dumb"); }
FWIW, I did #include <term.h>
and used lcurses
, since termcap is part of ncurses on Ubuntu/Debian?.
Compiling this with
$ gcc ltermcap tgetent_test.c o tgetent_test
and running it works flawlessly.
Libraries should in general be specified after the modules that use (parts of) them. This is (again) mandatory with newer Linux distros as you will know (cf. the Symmetrica and Singular changes for Ubuntu 11.10).
Some linkers seem to make a difference w.r.t. whether they find a static library [only] (or depending on whether LIBRARY_PATH
is set?  which sageenv
does).
However, the same gcc command with the Sage environment variables gives
$ ( source local/bin/sageenv; gcc ltermcap tgetent_test.c o tgetent_test ) /tmp/ccwDi3Oi.o: In function `main': tgetent_test.c:(.text+0x27): undefined reference to `tgetent' collect2: ld returned 1 exit status
This problem vanishes if you
 put
ltermcap
last (as one would expect), or unset LIBRARY_PATH
after sourcingsageenv
(in which case Sage'slibtermcap.a
of course isn't used), or both.
Anyway, I don't think this is related to our problem; Sage's readline shouldn't^{TM} use Sage's termcap library at all; on Ubuntu, libtermcap* is a symlink to libncurses*.
comment:34 Changed 8 years ago by
I confirm that ltermcap
should be last. With gcc 4.6.1:
tiramisu% gcc tgetent_test.c o tgetent_test ltermcap tiramisu% gcc ltermcap tgetent_test.c o tgetent_test /tmp/ccqQuCr3.o: In function `main': tgetent_test.c:(.text+0x2a): undefined reference to `tgetent' collect2: ld returned 1 exit status
Paul
comment:35 in reply to: ↑ 25 Changed 8 years ago by
Replying to jdemeyer:
On sage.math with:
 the new readline spkg from this ticket
 compiled with gcc4.2.4
 #12263 applied
the following happens (and all 3 conditions above are needed) [...]
Anything else that might affect this (besides #12263, which was merged into rc0), i.e., does the same happen with 4.8.alpha{5,6} + #12263 (with GCC 4.2.4 on Ubuntu 08.04 / sage.math
), and does my change (on top of readline6.2.p1) make the difference?
My current internet connection is quite poor, so I don't know if I can fully build Sage and experiment on sage.math
myself.
Otherwise you could try unsetting LIBRARY_PATH
in readline's spkginstall
(with the same configuration as above that segfaulted) and see whether that makes any difference. I didn't know that sageenv
sets LIBRARY_PATH
, so didn't expect that Sage's libtermcap might get picked up despite us intentionally not using I$SAGE_LOCAL/include
nor L$SAGE_LOCAL/lib
in readline's spkginstall
.
comment:36 Changed 8 years ago by
 Status changed from needs_work to needs_review
FWIW, I've made a p4 (changes not yet committed) that unsets LIBRARY_PATH
:
http://sage.math.washington.edu/home/leif/Sage/spkgs/readline6.2.p4.spkg
comment:37 Changed 8 years ago by
Ok, I've now successfully built Sage 4.8.alpha6 on sage.math
(with GCC 4.2.4); sage c True
works (doesn't segfault)
 with the vanilla installation
 with my new readline6.2.p4
 with my p4 and #12263 applied (i.e.,
TERM
unset).
Jeroen, can you check / confirm that it also works with your 4.8.rc1?
comment:38 Changed 8 years ago by
There's also a "debug" version which outputs some make
variables when building the shared library (modified patch to upstream):
http://sage.math.washington.edu/home/leif/Sage/spkgs/readline6.2.p4debug.spkg

src/shlib/Makefile.in
166 166 167 167 $(SHARED_READLINE): $(SHARED_OBJ) 168 168 $(RM) $@ 169 $(SHOBJ_LD) ${SHOBJ_LDFLAGS} ${SHLIB_XLDFLAGS} o $@ $(SHARED_OBJ) $(SHLIB_LIBS) 169 # $(SHOBJ_LD) ${SHOBJ_LDFLAGS} ${SHLIB_XLDFLAGS} o $@ $(SHARED_OBJ) $(SHLIB_LIBS) 170 @echo "**************************************************************************" 171 @echo "Sage: Shared readline library gets linked to \"$(TERMCAP_LIB)\"." 172 @echo 173 @echo "\$$(SHOBJ_LD)="$(SHOBJ_LD) 174 @echo "\$$(SHOBJ_LDFLAGS)="$(SHOBJ_LDFLAGS) 175 @echo "\$$(SHOBJ_XLDFLAGS)="$(SHOBJ_XLDFLAGS) 176 @echo 177 @echo "\$$(SHLIB_LIBS)="$(SHLIB_LIBS) 178 @echo "**************************************************************************" 179 $(SHOBJ_LD) ${SHOBJ_LDFLAGS} ${SHLIB_XLDFLAGS} o $@ $(SHARED_OBJ) $(SHLIB_LIBS) $(TERMCAP_LIB) 170 180 171 181 $(SHARED_HISTORY): $(SHARED_HISTOBJ) xmalloc.so xfree.so 172 182 $(RM) $@
comment:39 followup: ↓ 44 Changed 8 years ago by
 Keywords sd35.5 added
 Status changed from needs_review to needs_info
I tried http://sage.math.washington.edu/home/leif/Sage/spkgs/readline6.2.p4.spkg under Ubuntu 11.10 but still get:
tiramisu% ./sage   Sage Version 4.8.alpha5, Release Date: 20111221   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** WARNING: Readline services not available on this platform. WARNING: The autoindent feature requires the readline library
However I had previously installed the previous spkg (readline6.2.p3.spkg). Could it be that there was an interference between both? If so, how could I get a fresh Sage version without starting "make" from scratch?
Paul
comment:40 Changed 8 years ago by
I think I got to the bottom of the tgetent()
segmentation fault: it is a bug in the termcap library. Under normal circumstances, strcmp()
can be called with a NULL pointer argument.
comment:41 Changed 8 years ago by
See #12282 for the termcap issue.
comment:42 Changed 8 years ago by
 Dependencies set to #12282
 Status changed from needs_info to needs_review
comment:43 followup: ↓ 46 Changed 8 years ago by
 Status changed from needs_review to positive_review
comment:44 in reply to: ↑ 39 ; followup: ↓ 45 Changed 8 years ago by
Replying to zimmerma:
I tried http://sage.math.washington.edu/home/leif/Sage/spkgs/readline6.2.p4.spkg under Ubuntu 11.10 but still get:
tiramisu% ./sage   Sage Version 4.8.alpha5, Release Date: 20111221   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** WARNING: Readline services not available on this platform. WARNING: The autoindent feature requires the readline library
John Cremona reports that building Sage from scratch with the new readline p3 solves this warning.
comment:45 in reply to: ↑ 44 Changed 8 years ago by
Replying to jdemeyer:
Replying to zimmerma:
I tried http://sage.math.washington.edu/home/leif/Sage/spkgs/readline6.2.p4.spkg under Ubuntu 11.10 but still get:
... WARNING: Readline services not available on this platform. WARNING: The autoindent feature requires the readline library
John Cremona reports that building Sage from scratch with the new readline p3 solves this warning.
You just have to:
sudo aptget install libncurses5dev
as mentioned above (Re)install the readline spkg:
./sage f /path/to/readline6.2.p{2,3,4}
 Reinstall the Python spkg:
./sage f spkg/standard/python*
(or./sage f python2.6.4.p13
)
comment:46 in reply to: ↑ 43 ; followup: ↓ 49 Changed 8 years ago by
Replying to jdemeyer:
 status changed from needs_review to positive_review
Which spkg got the positive review?
I'd prefer also unsetting LIBRARY_PATH
in readline's spkginstall
(which the p4 does), since in any case we don't want to use Sage's static libtermcap there.
comment:47 Changed 8 years ago by
I've attached a diff between the p3 and the p4; the changes aren't yet committed though.
comment:48 Changed 8 years ago by
thanks Leif, I missed the last step (reinstalling the python spkg). It works now.
Paul
comment:49 in reply to: ↑ 46 Changed 8 years ago by
comment:50 Changed 8 years ago by
 Merged in set to sage4.8.rc0
 Resolution set to fixed
 Status changed from positive_review to closed
The problem isn't really R itself, but our readline spkg. (Cf. discussions on sagerelease where this
configure
error was reported for Ubuntu 11.10 systems that have libreadlinedev installed.)Here's a preliminary new readline spkg: