cannot compile smina in Cygwin
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I have been trying to compile Smina in Cygwin and I keep getting fatal error message saying openbabel/babelconfig.h: No such file or directory. (1) I removed my current version of Openbabel (2.4.1), and replaced it with version 2.0.0, but no change occurred. (2) I thought maybe I can comment out the lines referring to openbabel in src/main/main.cpp, but this does not work because I get into trouble with src/lib/obmolopener.h line mentioning openlabel/obconversion.h, for instance.
Could this be because I am using Cygwin64? Your help will be greatly appreciated. Hiroshi
You need to specify the include path to the openbabel install with -I. Not sure that will be enough to compile under cygwin though - never tried it.
Thank you very much for so promptly helping me. I have now compiled properly openbabel 2.4.1 in Cygwin and have the path included, so that I do not get the error message mentioned above.
However, I still get one error concerning openbabel plugin.h, where on line 44 it says {return strcascomp(p1,p2)<0}, that the string case comparison function strcascomp is not declared in this scope. "make" did not say that compilation was stopped, but apparently it did because I see nothing in the /usr/local directory. I would be extremely grateful if you could tell me how I could get out of this mess. Regards, Hiroshi
Seems like a cygwin specific problem. I found this by googling "strcasecomp cygwin":
https://stackoverflow.com/questions/7248509/strcasecmp-was-not-declared-in-this-scope?rq=1
Thank you again. The "strcasecomp" problem was solved by the suggestion there. But now the compiler is complaining about "@" in plugin.h (from line 37). Googling taught me that "@" is not allowed in C. Could you tell me what to do? The offending area of plugin.h reads as follows.
namespace OpenBabel
{
/@addtogroup plugins Plugins
/@{
/ @brief Case insensitive string comparison for Plugin Typekey
struct OBERROR etc.
My apologies for taking up your time!! Hiroshi
Looking at the source on github (https://github.com/openbabel/openbabel/blob/master/include/openbabel/plugin.h) those are all lines that should be commented out (there should be more than one slash).
Thank you. After commentng out these lines, there was still the old strcascomp problem now in plugin.h. This was surprising because at the top there was there was the #include <string.h> line. However, I finally solved it by changing <string.h> to <strings.h>. The compilation went to completion, although there were lots of minor complaints (notes), "deprecating" certain items.
However, I still cannot find the compiled smina program. Where should I look?
Please pardon my ignorance. Hiroshi
It should be in the build directory with the makefile, e.g. smina/build/linux/release
Dear Dr. Koes,
Indeed there are all these compiled .o files, but I don't know what I should do next. There is no "Install" information in the Makefile, and thus install or install smina does not work. Hiroshi
If there is no smina binary, then it did not successfully compile. Perhaps look more carefully for an error message?