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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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hapFabia_1.2.1.tar.gz
StartedAt: 2013-05-01 06:43:59 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 06:46:11 -0700 (Wed, 01 May 2013)
EllapsedTime: 132.1 seconds
RetCode: 0
Status:  OK 
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'hapFabia/DESCRIPTION' ... OK
* this is package 'hapFabia' version '1.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'hapFabia' can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'hapFabia/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("+--------------------------+          #    #    ##    #####     \n",     "|#.....#...#.......#.#....#|          #    #   #  #   #    #    \n",     "|#.....#...#.......#.#....#|          ######  #    #  #    #    \n",     "|#.....#...#...............|          #    #  ######  #####     \n",     "|#.....#...#.......#.#....#|          #    #  #    #  #         \n",     "|#.....#...#...............|          #    #  #    #  #         \n",     "|#.....#...#.......#.#....#|  #######                           \n",     "|..................#.#....#|  #         ##    #####   #    ##   \n",     "|#.....#...#.......#.#....#|  #        #  #   #    #  #   #  #  \n",     "|..................#.#....#|  #####   #    #  #####   #  #    # \n",     "|#.....#...#.......#.#....#|  #       ######  #    #  #  ###### \n",     "|#.....#...#.......#.#....#|  #       #    #  #    #  #  #    # \n",     "+--------------------------+  #       #    #  #####   #  #    # \n")
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "FABIA: Factor Analysis for Bicluster Acquisition,", "\n",     "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html",     "\n\n", "hapFabia Package Version ", version, "\n")

See section 'Good practice' in '?.onAttach'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [38s/45s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
iterateIntervals 16.972  1.078  24.107
hapFabia          7.920  0.253   8.493
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/00check.log'
for details.

hapFabia.Rcheck/00install.out:

* installing *source* package 'hapFabia' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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 -ggdb -O0 -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.Rcheck/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)

hapFabia.Rcheck/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.8650.1191.070
IBDsegmentList-class0.1050.0050.114
IBDsegmentList2excel0.0320.0030.034
analyzeIBDsegments0.0840.0040.089
compareIBDsegmentLists0.1500.0050.158
extractIBDsegments0.1170.0120.136
findDenseRegions0.0190.0010.020
hapFabia7.9200.2538.493
hapFabiaVersion0.0090.0020.011
identifyDuplicates0.0870.0170.116
iterateIntervals16.972 1.07824.107
makePipelineFile0.0280.0110.041
matrixPlot0.0230.0070.030
mergeIBDsegmentLists0.1480.0160.172
plotIBDsegment0.5340.1280.757
setAnnotation0.1320.0350.188
setStatistics0.1040.0200.126
sim0.0060.0060.012
simulateIBDsegments0.0080.0070.016
simulateIBDsegmentsFabia3.5220.2814.180
split_sparse_matrix0.0420.0440.089
toolsFactorizationClass2.1610.1052.340
vcftoFABIA0.0460.0540.102