Hello,
I am trying to build openbabel on a CentOS cluster and am having problems.
When I execute:
cmake .. -DCMAKE_INSTALL_PREFIX=../../openbabel-build
> -DEIGEN3_INCLUDE_DIR=../../eigen-build/3.2.5/
I obtain the following in CMakeError.log. Does anyone have any suggestions
on how to proceed?
Determining if the include file conio.h exists failed with the following
> output:
> Change Dir:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec842003284/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec842003284.dir/build.make
> CMakeFiles/cmTryCompileExec842003284.dir/build
> gmake[1]: Entering directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> /home/eric.smoll/cmake-3.2.2-Linux-x86_64/bin/cmake -E
> cmake_progress_report
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object
> CMakeFiles/cmTryCompileExec842003284.dir/CheckIncludeFile.c.o
> /usr/bin/cc -o
> CMakeFiles/cmTryCompileExec842003284.dir/CheckIncludeFile.c.o -c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c:1:19:
> error: conio.h: No such file or directory
> gmake[1]: ***
> [CMakeFiles/cmTryCompileExec842003284.dir/CheckIncludeFile.c.o] Error 1
> gmake[1]: Leaving directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec842003284/fast] Error 2
>
> Determining if the rint exist failed with the following output:
> Change Dir:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec1912286806/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1912286806.dir/build.make
> CMakeFiles/cmTryCompileExec1912286806.dir/build
> gmake[1]: Entering directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> /home/eric.smoll/cmake-3.2.2-Linux-x86_64/bin/cmake -E
> cmake_progress_report
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object
> CMakeFiles/cmTryCompileExec1912286806.dir/CheckSymbolExists.c.o
> /usr/bin/cc -o
> CMakeFiles/cmTryCompileExec1912286806.dir/CheckSymbolExists.c.o -c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
> Linking C executable cmTryCompileExec1912286806
> /home/eric.smoll/cmake-3.2.2-Linux-x86_64/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec1912286806.dir/link.txt --verbose=1
>
>
>
>
> /usr/bin/cc
> CMakeFiles/cmTryCompileExec1912286806.dir/CheckSymbolExists.c.o -o
> cmTryCompileExec1912286806 -rdynamic
> CMakeFiles/cmTryCompileExec1912286806.dir/CheckSymbolExists.c.o: In
> function `main':
> CheckSymbolExists.c:(.text+0xc): undefined reference to `rint'
> collect2: ld returned 1 exit status
> gmake[1]: *** [cmTryCompileExec1912286806] Error 1
> gmake[1]: Leaving directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec1912286806/fast] Error 2
> File
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include <math.h>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef rint
> return ((int*)(&rint))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
> Determining if the sranddev exist failed with the following output:
> Change Dir:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec1796022829/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1796022829.dir/build.make
> CMakeFiles/cmTryCompileExec1796022829.dir/build
> gmake[1]: Entering directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> /home/eric.smoll/cmake-3.2.2-Linux-x86_64/bin/cmake -E
> cmake_progress_report
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object
> CMakeFiles/cmTryCompileExec1796022829.dir/CheckSymbolExists.c.o
> /usr/bin/cc -o
> CMakeFiles/cmTryCompileExec1796022829.dir/CheckSymbolExists.c.o -c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> In function ‘main’:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:
> error: ‘sranddev’ undeclared (first use in this function)
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:
> error: (Each undeclared identifier is reported only once
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:
> error: for each function it appears in.)
> gmake[1]: ***
> [CMakeFiles/cmTryCompileExec1796022829.dir/CheckSymbolExists.c.o] Error 1
> gmake[1]: Leaving directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec1796022829/fast] Error 2
> File
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include <stdlib.h>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef sranddev
> return ((int*)(&sranddev))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
> Performing C SOURCE FILE Test SCANDIR_NEEDS_CONST failed with the
> following output:
> Change Dir:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp
> Run Build Command:"/usr/bin/gmake" "cmTryCompileExec1246088137/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1246088137.dir/build.make
> CMakeFiles/cmTryCompileExec1246088137.dir/build
> gmake[1]: Entering directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> /home/eric.smoll/cmake-3.2.2-Linux-x86_64/bin/cmake -E
> cmake_progress_report
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/CMakeFiles
> 1
> Building C object CMakeFiles/cmTryCompileExec1246088137.dir/src.c.o
> /usr/bin/cc -DSCANDIR_NEEDS_CONST -Werror -o
> CMakeFiles/cmTryCompileExec1246088137.dir/src.c.o -c
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/src.c
> cc1: warnings being treated as errors
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/src.c:
> In function ‘main’:
> /mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp/src.c:7:
> error: passing argument 3 of ‘scandir’ from incompatible pointer type
> /usr/include/dirent.h:252: note: expected ‘int (*)(const struct dirent *)’
> but argument is of type ‘int (*)(struct dirent *)’
> gmake[1]: *** [CMakeFiles/cmTryCompileExec1246088137.dir/src.c.o] Error 1
> gmake[1]: Leaving directory
> `/mnt/lustrefs/store/group/kaptonlab/openbabel-2.3.2/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec1246088137/fast] Error 2
> Source file was:
> #include <sys/types.h>
> #include <dirent.h>
> int main(){
> extern int matchFiles (struct dirent *entry_p);
> struct dirent **entries_pp;
> int count = scandir ("./", &entries_pp, matchFiles, 0);
> return count;
> }
Best,
Eric
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