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23 bytes added
, 10:16, 28 March 2014
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| 1) libStatGen/Makefiles/Makefile.src, edit the settings for OPT_BUILD, DEBUG_BUILD, and PROFILE_BUILD to be (the new part is in bold): | | 1) libStatGen/Makefiles/Makefile.src, edit the settings for OPT_BUILD, DEBUG_BUILD, and PROFILE_BUILD to be (the new part is in bold): |
− | OPT_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_OPT) $(OBJECTS_OPT) $(USER_LIBS) $(REQ_LIBS_OPT) -lm $(ZLIB_LIB) $(OTHER_LIBS) | + | OPT_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_OPT) $(OBJECTS_OPT) $(USER_LIBS) $(REQ_LIBS_OPT) -lm $(ZLIB_LIB) '''$(OTHER_LIBS)''' |
− | DEBUG_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_DEBUG) $(OBJECTS_DEBUG) $(USER_LIBS) $(REQ_LIBS_DEBUG) -lm $(ZLIB_LIB) $(OTHER_LIBS) | + | DEBUG_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_DEBUG) $(OBJECTS_DEBUG) $(USER_LIBS) $(REQ_LIBS_DEBUG) -lm $(ZLIB_LIB) '''$(OTHER_LIBS)''' |
− | PROFILE_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_PROFILE) $(OBJECTS_PROFILE) $(USER_LIBS) $(REQ_LIBS_PROFILE) -lm $(ZLIB_LIB) $(OTHER_LIBS) | + | PROFILE_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_PROFILE) $(OBJECTS_PROFILE) $(USER_LIBS) $(REQ_LIBS_PROFILE) -lm $(ZLIB_LIB) '''$(OTHER_LIBS)''' |
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| 2) raremetal/src/Makefile, add: (I added it on the line right after USER_LIBS is defined.) | | 2) raremetal/src/Makefile, add: (I added it on the line right after USER_LIBS is defined.) |
− | OTHER_LIBS = -lgfortran | + | OTHER_LIBS = -lgfortran |
− | | + | NOTE: this has been fixed by identifying a bug in makefile. If you still see the same error message, please try the above solutions. |
− | NOTE: this has been fixed by idenifying a bug in makefile. If you still see the same error message, please try the above solutions. | |
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| ===error while loading shared libraries=== | | ===error while loading shared libraries=== |
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| If you are using version 0.4.4 and under, please go to our wiki page to download the newest version [[[RAREMETAL]]]. There was a bug in makefile in older versions of RAREMETAL that could cause this error and it has been fixed. For a quick fix, please go to /raremetal/src and open "Makefile". Then comment out the lines at the bottom of raremetal/src/Makefile that set LD_LIBRARY_PATH. Try compiling and see if it works. | | If you are using version 0.4.4 and under, please go to our wiki page to download the newest version [[[RAREMETAL]]]. There was a bug in makefile in older versions of RAREMETAL that could cause this error and it has been fixed. For a quick fix, please go to /raremetal/src and open "Makefile". Then comment out the lines at the bottom of raremetal/src/Makefile that set LD_LIBRARY_PATH. Try compiling and see if it works. |
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| + | ==RUNTIME ERRORS== |
| ===error: BGZF EOF marker is missing in xxx.vcf.gz=== | | ===error: BGZF EOF marker is missing in xxx.vcf.gz=== |
| Loading input files... | | Loading input files... |
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| This problem has been solved. If you are using version 0.4.5 or older, please download the newest version [[[RAREMETALWORKER]]], and then in your command line, add --noeof. If you still see the error message, then you need to check if your bgzip has been updated to current version. | | This problem has been solved. If you are using version 0.4.5 or older, please download the newest version [[[RAREMETALWORKER]]], and then in your command line, add --noeof. If you still see the error message, then you need to check if your bgzip has been updated to current version. |
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− | ==RUNTIME ERRORS==
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| ===recommended strategies for debugging=== | | ===recommended strategies for debugging=== |