I am hitting problems making the sage package version 4.7.1 on the above named system.
The first problem which I hit was a readline problem for the R library. While the sage installer was running configure for the R library package it answered the following - checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... no and things soon quit after that with an error. I added some debugging statements in the configure file, in order to try to find out what was going wrong and found that there was indeed a difference, when running make in the SAGE environment, versus running make in the normal linux environment. Running in the SAGE environment, the configure file shows checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... failed here line 21665 conftest.c ac_c_werror_flag = || conftest.err file: -rw-r--r-- 1 root root 765 Oct 3 09:14 conftest.err -------------------------------------------------------------------------- /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tputs' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tgoto' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tgetflag' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `UP' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tgetent' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tgetnum' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `PC' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `tgetstr' /root/sage-4.7.1/local/lib/../lib/libreadline.so: undefined reference to `BC' collect2: ld returned 1 exit status -------------------------------------------------------------------------- conftest file: ls: cannot access conftest: No such file or directory value of as_text_x |test -x| no So there are undefined references hanging here, when referencing to the local Sage library in /local/lib A good configure run displays checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... success here line 21657 conftest.c ac_link = |$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5| ac_c_werror_flag = || conftest.err file: -rw-r--r-- 1 root root 0 Oct 3 09:12 conftest.err conftest file: -rwxr-xr-x 1 root root 9528 Oct 3 09:12 conftest value of as_text_x |test -x| yes so the conftest.err file is empty, no errors indicated. I took the time to read some of the posts about readline problems and adopted William Stein's temporary fix, of making the libreadline libraries invisible in the local/lib area, and recompiling. This indeed fixed the problem and so the Sage installer now did successfully install the R library package and continued on with several other packages. However I now have hit a problem with the Singular install that I don't think will be solved as easily. While running make under the SAGE environment, a snag is hit - ../kernel/libkernel.a(mod_raw.o): In function `dynl_open': /root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12/src/kernel/mod_raw.cc: 217: undefined reference to `dlopen' ../kernel/libkernel.a(mod_raw.o): In function `dynl_sym': /root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12/src/kernel/mod_raw.cc: 228: undefined reference to `dlsym' ../kernel/libkernel.a(mod_raw.o): In function `dynl_close': /root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12/src/kernel/mod_raw.cc: 233: undefined reference to `dlclose' ../kernel/libkernel.a(mod_raw.o): In function `dynl_error': /root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12/src/kernel/mod_raw.cc: 238: undefined reference to `dlerror' collect2: ld returned 1 exit status make[4]: *** [iparith.inc] Error 1 make[4]: Leaving directory `/root/sage-4.7.1/spkg/build/ singular-3-1-1-4.p12/src/Singular' make[3]: *** [install] Error 1 make[3]: Leaving directory `/root/sage-4.7.1/spkg/build/ singular-3-1-1-4.p12/src' make[2]: *** [/root/sage-4.7.1/local/bin/Singular-3-1-1] Error 2 make[2]: Leaving directory `/root/sage-4.7.1/spkg/build/ singular-3-1-1-4.p12/src' Unable to build Singular. real 5m40.579s user 5m28.657s sys 0m13.977s sage: An error occurred while installing singular-3-1-1-4.p12 Please email sage-devel http://groups.google.com/group/sage-devel explaining the problem and send the relevant part of of /root/sage-4.7.1/install.log. Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12 and type 'make check' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/root/sage-4.7.1/spkg/build/singular-3-1-1-4.p12' && '/root/ sage-4.7.1/sage' -sh) When you are done debugging, you can type "exit" to leave the subshell. make[1]: *** [installed/singular-3-1-1-4.p12] Error 1 make[1]: Leaving directory `/root/sage-4.7.1/spkg' real 5m43.153s user 5m31.181s sys 0m14.177s Error building Sage. make: *** [build] Error 1 This error is puzzling to me, because the make_raw.cc package specifically provides "dlopen" "dlsym" "dlclose" and "dlerror" function definitions, although it seems that this package does make a call to the currently installed libdl.a package on the user's system and has to use the header file "ldfcn.h". I did find 2 libdl libraries under the usr folder, but not in the normal custom place of / usr/lib or /usr/local/lib so perhaps there might be a library path problem? I did drop the two static libdl libraries into the local SAGE library folder, hoping that this might fix the linker problem, but to no avail. Whether I try to compile singular inside the SAGE environment, or the normal linux environment, it still fails, hinting that something might actually be wrong with the Singular kernel code itself, not with the Sage installer. There are not too many Sage packages left to build, the ATLAS library build took a long time, so I would like to continue on if possible and obtain a partially working Sage package on the Colfax HPC, if possible. SIDENOTE: For the most part, running make with the -j flag for parallel compiling sped up the Sage install immensely, and if a particular package defaulted, I could rerun "make -j" again and usually get around the bug. However I did notice that ATLAS had to be built in the single threaded mode, since it runs timing tests periodically, and running a parallel compile messed this up and broke the ATLAS library compile, so I was forced to compile that library in single proc mode to get it successfully to build and then build the subsequent packages depending upon it. I would appreciate any comments on how to fix the Singular build problem, or how to bypass it and continue on with the few remaining packages, so that I can get a mostly function sage executable. Thanks! Randall -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
