@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.16.0

-Date: 2017-07-12

+Version: 1.16.1

+Date: 2018-05-31

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

deleted file mode 100644

@@ -1,35 +0,0 @@

-AC_PREREQ([2.65])

-

-AC_INIT("CNEr")

-

-## Checks for libraries

-

-

-## Checks for headers

-AC_CHECK_HEADERS([arpa/inet.h netinet/in.h signal.h stdio.h stdlib.h 

-                  stdarg.h string.h ctype.h sys/types.h sys/stat.h 

-                  strings.h fcntl.h assert.h setjmp.h sys/time.h math.h 

-                  errno.h unistd.h libgen.h pthread.h sys/socket.h 

-                  netdb.h utime.h limits.h pwd.h termios.h 

-                  sys/wait.h regex.h dirent.h sys/file.h])

-

-## Checks for typedefs, structures, and compiler characteristics.

-AC_HEADER_STDBOOL

-AC_C_INLINE

-AC_TYPE_OFF_T

-AC_TYPE_PID_T

-AC_TYPE_SIZE_T

-AC_TYPE_SSIZE_T

-AC_TYPE_UID_T

-

-## Checks for library functions.

-AC_FUNC_FORK

-AC_FUNC_MALLOC

-AC_FUNC_MKTIME

-AC_FUNC_REALLOC

-AC_FUNC_STRTOD

-AC_CHECK_FUNCS([bzero dup2 getcwd gethostbyname gettimeofday memmove 

-                memset mkdir regcomp select socket sqrt strcasecmp strchr 

-                strcspn strdup strerror strrchr strspn strstr uname])

-

-AC_OUTPUT(src/Makevars)

similarity index 96%

rename from src/alignment.c

rename to inst/obsolete/alignment.c

@@ -45,12 +45,11 @@ SEXP subAlignment(SEXP axttStart, SEXP axttEnd, SEXP axttSym,

       }

       if(INTEGER(subtStart) == INTEGER(axttStart) + j - nrGapsTarget){

         cpStartTarget = j;

-        INTEGER(newqStart) = j + INTEGER(axtqStart) 

+        INTEGER(newqStart) = j + INTEGER(axtqStart);

       }

       if(INTEGER(subtEnd) == INTEGER(axttStart) + j - nrGapsTarget){

-        cpENdTarget = j;

+        cpEndTarget = j;

       }

-      

     }

     Rprintf("\n");

   }