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Package 307/671HostnameOS / ArchBUILDCHECKBUILD BIN
hapFabia 1.2.1
Sepp Hochreiter
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/hapFabia
Last Changed Rev: 75640 / Revision: 76155
Last Changed Date: 2013-04-14 08:37:12 -0700 (Sun, 14 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: hapFabia
Version: 1.2.1
Command: rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hapFabia_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R hapFabia.buildbin-libdir
StartedAt: 2013-05-01 12:30:55 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:31:09 -0700 (Wed, 01 May 2013)
EllapsedTime: 13.3 seconds
RetCode: 0
Status:  OK 
PackageFile: hapFabia_1.2.1.tgz
PackageFileSize: 1.63 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.2.1.tar.gz'
>>>>>>> 

* installing *source* package 'hapFabia' ...
rmdir: inst/commandLine/i386: No such file or directory
rmdir: inst/commandLine/x86_64: No such file or directory
rmdir: inst/commandLine/ppc: No such file or directory
rmdir: inst/commandLine/ppc64: No such file or directory
rmdir: inst/commandLine: No such file or directory
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c interfaceR.c -o interfaceR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c split_sparse_matrixB.c -o split_sparse_matrixB.o
split_sparse_matrixB.c:101:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    char **fileN = calloc(parts, sizeof(char *));
                   ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:102:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fileN[0] =  calloc((long) 200*parts, sizeof(char));
                ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
split_sparse_matrixB.c:108:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *startP = calloc(parts , sizeof(int));
                  ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:109:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *endP = calloc(parts , sizeof(int));
                ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:150:27: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    double *Lval = calloc((long) snps , sizeof(double));
                   ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
split_sparse_matrixB.c:152:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *Lind = calloc((long) snps , sizeof(int));
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
split_sparse_matrixB.c:283:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    char **fileN1 = calloc(parts, sizeof(char *));
                    ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:284:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fileN1[0] =  calloc((long) 200*parts, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c:68:11: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'ssize_t' (aka 'long') [-Wsign-conversion]
   return idx;
   ˜˜˜˜˜˜ ^˜˜
vcftoFABIAB.c:126:7: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  eps=0.6;
     ˜^˜˜
vcftoFABIAB.c:196:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g1 = calloc(individuals, sizeof(unsigned short *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:197:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g1[0] =  calloc((long) individuals*snps, sizeof(unsigned short));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:202:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g2 = calloc(individuals, sizeof(unsigned short *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:203:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g2[0] =  calloc((long) individuals*snps, sizeof(unsigned short));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:209:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      ds = calloc(individuals, sizeof(float *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:210:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      ds[0] =  calloc((long) individuals*snps, sizeof(float));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:218:22: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      chrom = calloc((long) snps , sizeof(unsigned short));
              ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:219:20: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      pos = calloc((long) snps , sizeof(unsigned int));
            ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:220:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      freq = calloc((long) snps , sizeof(float));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:221:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      Lval = calloc((long) snps , sizeof(float));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:222:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      Lind = calloc((long) snps , sizeof(unsigned int));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:223:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      change = calloc((long) snps , sizeof(unsigned short));
               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:228:22: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      major = calloc(snps, sizeof(char *));
              ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:229:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      major[0] =  calloc((long) 200*snps, sizeof(char));
                  ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:235:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
     minor = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:236:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      minor[0] =  calloc((long) 200*snps, sizeof(char));
                  ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:242:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      snpName = calloc(snps, sizeof(char *));
                ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:243:37: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      snpName[0] =  calloc((long) 50*snps, sizeof(char));
                    ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:250:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      filter = calloc(snps, sizeof(char *));
               ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:251:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      filter[0] =  calloc((long) 20*snps, sizeof(char));
                   ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:258:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qual = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:259:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qual[0] =  calloc((long) 20*snps, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:265:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      info = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:266:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      info[0] =  calloc((long) 200*snps, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:273:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      format = calloc(snps, sizeof(char *));
               ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:274:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      format[0] =  calloc((long) 20*snps, sizeof(char));
                   ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:460:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
          freq[j] = (float) (1.0*ig)/(1.0*individuals);
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:469:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  ds[i][j] = 1.0 - ds[i][j];
                           ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:473:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
          freq[j] = (float) (1.0*ig)/(2.0*individuals);
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:482:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  ds[i][j] = 2.0 - ds[i][j];
                           ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:555:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:574:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:615:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:653:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
36 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -mtune=native -g -O2 -Wall -pedantic -Wconversion
./commandLine/split_sparse_matrix.c:9:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  printf(RSformat);
         ^˜˜˜˜˜˜˜
1 warning generated.
clang -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -mtune=native -g -O2 -Wall -pedantic -Wconversion
split_sparse_matrixB.c:101:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    char **fileN = calloc(parts, sizeof(char *));
                   ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:102:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fileN[0] =  calloc((long) 200*parts, sizeof(char));
                ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
split_sparse_matrixB.c:108:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *startP = calloc(parts , sizeof(int));
                  ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:109:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *endP = calloc(parts , sizeof(int));
                ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:150:27: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    double *Lval = calloc((long) snps , sizeof(double));
                   ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
split_sparse_matrixB.c:152:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    int *Lind = calloc((long) snps , sizeof(int));
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
split_sparse_matrixB.c:283:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    char **fileN1 = calloc(parts, sizeof(char *));
                    ˜˜˜˜˜˜ ^˜˜˜˜
split_sparse_matrixB.c:284:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fileN1[0] =  calloc((long) 200*parts, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
8 warnings generated.
clang ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
clang -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -mtune=native -g -O2 -Wall -pedantic -Wconversion
./commandLine/vcftoFABIA.c:10:10: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  printf(RSformat);
         ^˜˜˜˜˜˜˜
1 warning generated.
clang -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -mtune=native -g -O2 -Wall -pedantic -Wconversion
vcftoFABIAB.c:68:11: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'ssize_t' (aka 'long') [-Wsign-conversion]
   return idx;
   ˜˜˜˜˜˜ ^˜˜
vcftoFABIAB.c:126:7: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  eps=0.6;
     ˜^˜˜
vcftoFABIAB.c:196:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g1 = calloc(individuals, sizeof(unsigned short *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:197:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g1[0] =  calloc((long) individuals*snps, sizeof(unsigned short));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:202:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g2 = calloc(individuals, sizeof(unsigned short *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:203:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      g2[0] =  calloc((long) individuals*snps, sizeof(unsigned short));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:209:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      ds = calloc(individuals, sizeof(float *));
           ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:210:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      ds[0] =  calloc((long) individuals*snps, sizeof(float));
               ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:218:22: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      chrom = calloc((long) snps , sizeof(unsigned short));
              ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:219:20: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      pos = calloc((long) snps , sizeof(unsigned int));
            ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:220:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      freq = calloc((long) snps , sizeof(float));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:221:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      Lval = calloc((long) snps , sizeof(float));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:222:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      Lind = calloc((long) snps , sizeof(unsigned int));
             ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:223:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      change = calloc((long) snps , sizeof(unsigned short));
               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:228:22: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      major = calloc(snps, sizeof(char *));
              ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:229:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      major[0] =  calloc((long) 200*snps, sizeof(char));
                  ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:235:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
     minor = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:236:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      minor[0] =  calloc((long) 200*snps, sizeof(char));
                  ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:242:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      snpName = calloc(snps, sizeof(char *));
                ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:243:37: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      snpName[0] =  calloc((long) 50*snps, sizeof(char));
                    ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:250:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      filter = calloc(snps, sizeof(char *));
               ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:251:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      filter[0] =  calloc((long) 20*snps, sizeof(char));
                   ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:258:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qual = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:259:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qual[0] =  calloc((long) 20*snps, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:265:21: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      info = calloc(snps, sizeof(char *));
             ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:266:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      info[0] =  calloc((long) 200*snps, sizeof(char));
                 ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:273:23: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      format = calloc(snps, sizeof(char *));
               ˜˜˜˜˜˜ ^˜˜˜
vcftoFABIAB.c:274:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      format[0] =  calloc((long) 20*snps, sizeof(char));
                   ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
vcftoFABIAB.c:460:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
          freq[j] = (float) (1.0*ig)/(1.0*individuals);
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:469:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  ds[i][j] = 1.0 - ds[i][j];
                           ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:473:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
          freq[j] = (float) (1.0*ig)/(2.0*individuals);
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:482:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  ds[i][j] = 2.0 - ds[i][j];
                           ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
vcftoFABIAB.c:555:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:574:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:615:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
vcftoFABIAB.c:653:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                Lind[ig] = j;
                         ˜ ^
36 warnings generated.
clang ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hapFabia)


>>>>>>> 
>>>>>>> FIXING LINKS FOR hapFabia.buildbin-libdir/hapFabia/libs//hapFabia.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "hapFabia.buildbin-libdir/hapFabia/libs//hapFabia.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs//hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs//hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "hapFabia.buildbin-libdir/hapFabia/libs//hapFabia.so"