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--- archive:bioinformatic_tools:allpaths [2010/04/19 05:14]
jstjohn
+++ archive:bioinformatic_tools:allpaths [2010/04/19 06:21]
jstjohn
@@ Line 46: / Line 46: @@
 Installed gcc-4.5! (had to do it myself, the sys admins wouldn't try)
-Note, if you compile with gcc-4.5 (or any of the other cc/c++-4.5) you will need to do one of the following:
+The gcc/g++-4.5 libraries are installed in:
-----------------------------------------------------------------------
+  /campusdata/BME235/lib
-Libraries have been installed in:
+  /campusdata/BME235/lib64
-   /campusdata/BME235/lib/../lib64
-If you ever happen to want to link against installed libraries
+To compile with the gcc 4.5 compilers you need to have your environment properly set up so that everything knows where to look for the linked libraries. I did this by setting my LD_LIBRARY_PATH variable as follows in my .profile
-in a given directory, LIBDIR, you must either use libtool, and
-specify the full pathname of the library, or use the `-LLIBDIR'
-flag during linking and do at least one of the following:
-   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
-     during execution
-   - add LIBDIR to the `LD_RUN_PATH' environment variable
-     during linking
-   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
-   - have your system administrator add LIBDIR to `/etc/ld.so.conf'
-See any operating system documentation about shared libraries for
+  LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH
-more information, such as the ld(1) and ld.so(8) manual pages.
+  export LD_LIBRARY_PATH
-----------------------------------------------------------------------
+Note if you want to run the install via a script, an example script that sets up environmental variables is here:
-While attempting to install Allpaths I get an error right away for all methods other than setting
+  /campusdata/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh
+I have encountered a new error much further along in the compilation.  To view the error see the last 40 lines of file:
+  /campus/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh.o2730
+  /campusdata/BME235/programs/allpaths/allpaths3-3.2/src/paths/MuxWalkGraph.cc:740: undefined reference to `digraphE<KmerPath>::TransferEdges(int, int, unsigned char)'
-  LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64
 ===== References =====
 <refnotes>notes-separator: none</refnotes>
 ~~REFNOTES cite~~

Banana Slug Genomics

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