LibStatGen Troubleshooting

Possible Compile Errors

The following are a list of compile errors that have been encountered with recommendations on what they mean and how to fix them.

Compile Error on first time building

Record the error.

Try to recompile and see if that fixes the problem. If it does fix the compile error, let me know what the original error was so I can fix the dependency so it compiles in the correct order.

NOTE: In the latest version (in development, after 0.1.4), I think I have this fixed.

GenomeSequence.h:30:57: error: openssl/md5.h: No such file or directory

GenomeSequence requires md5 logic and makes calls to methods defined in md5.h which is found in the openssl library.

The header files are included in the development version of the package.

The package may be called something like: openssl-devel or libssl-dev (on ubuntu).

error: Sam[filename].h: No such file or directory or "'Sam[classname]' has not been declared"

This error and other, similar errors with "Sam....h: No such file or directory" or "'Sam...' has not been declared" typically means that the library build failed. Check for a previous error in your compile.

A successful compile of the library will publish SamFile.h and all the other header files from the library into samtools/lib/include. If one of the programs within the statgen repository fails to compile with one of these errors, then the library did not successfully publish the header files and did not successfully byild.

make test produces messages like "ERROR: Missing required tag: LN." and "Can't modify the key tag, ID from pid to pid1"

These messages are currently expected. Some of the tests run by 'make test' test error conditions to make sure they are handled properly. These error conditions print messages to the screen about the errors. These messages are expected and are not a failure of 'make test'.

GenomeSequence.cpp:552: warning: converting to `int' from `double'

This has been fixed in versions after 3/1/11.

Update statgen/lib/general/GenomeSequence.cpp line 552 to the following:

            newPercent = (int) (1.0 * fastaIndex / fastaDataSize) * 100;

Complaints about unknown -Wno-unused-result option in lib/general/Makefile

This has been fixed in versions after 3/1/11.

Update stagen/lib/general/Makefile line 17 to the following:

WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)