Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 100/671HostnameOS / ArchBUILDCHECKBUILD BIN
casper 1.1.1
David Rossell
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/casper
Last Changed Rev: 75744 / Revision: 76155
Last Changed Date: 2013-04-17 06:40:38 -0700 (Wed, 17 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 [ WARNINGS ] OK 

Summary

Package: casper
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch casper_1.1.1.tar.gz
StartedAt: 2013-05-01 03:19:42 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:27:28 -0700 (Wed, 01 May 2013)
EllapsedTime: 466.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: casper.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/casper.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 'casper/DESCRIPTION' ... OK
* this is package 'casper' version '1.1.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'casper' can be installed ... [50s/53s] WARNING
Found the following significant warnings:
  casper.cpp:367:14: warning: variable 'ans' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/casper.Rcheck/00install.out' for details.
* 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
casperSim: warning in sample(as.numeric(names(distrs@lenDis)), p =
  distrs@lenDis/sum(distrs@lenDis), size = sum(nSimReads), replace =
  T): partial argument match of 'p' to 'prob'
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [42s/43s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
calcExp 10.882      1  12.273
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/casper.Rcheck/00check.log'
for details.

casper.Rcheck/00install.out:

* installing *source* package 'casper' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c casper.cpp -o casper.o
casper.cpp:367:14: warning: variable 'ans' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (method==2) {
             ^˜˜˜˜˜˜˜˜
casper.cpp:375:10: note: uninitialized use occurs here
  return ans;
         ^˜˜
casper.cpp:367:10: note: remove the 'if' if its condition is always true
  } else if (method==2) {
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
casper.cpp:361:13: note: initialize the variable 'ans' to silence this warning
  double ans;
            ^
             = 0.0
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cstat.cpp -o cstat.o
cstat.cpp:989:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a = (double ***) malloc(n1 * sizeof(double **));
                          ^˜ ˜
cstat.cpp:995:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0] = (double **) malloc(n1 * n2 * sizeof(double *));
                            ˜˜˜^˜˜˜ ˜
cstat.cpp:1002:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0][0] = (double *) malloc(n1 * n2 * n3 * sizeof(double));
                              ˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.cpp:1082:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a = (int ***) malloc(n1 * sizeof(int **));
                       ^˜ ˜
cstat.cpp:1088:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0] = (int **) malloc(n1 * n2 * sizeof(int *));
                         ˜˜˜^˜˜˜ ˜
cstat.cpp:1095:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  a[0][0] = (int *) malloc(n1 * n2 * n3 * sizeof(int));
                           ˜˜˜˜˜˜˜˜^˜˜˜ ˜
cstat.cpp:1208:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    n = (long)(*a - 1.25e0);
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.cpp:1974:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
    else if (sum) ii=i; //Nonzero element encountered, from now we do sums in the loop above.
         ˜˜  ^˜˜
cstat.cpp:2085:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
      if (d[i]) {
      ˜˜  ^˜˜˜
cstat.cpp:2178:11: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort (v, size, sizeof (double), dcompare);
˜˜˜˜˜     ^˜˜˜
cstat.cpp:2627:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ans= poibinProbs->at(x);
         ˜˜˜˜˜˜˜˜˜˜˜     ^
cstat.cpp:2631:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      for (int k=0; k < nsuccessProbs; k++) ans += nvars->at(k) * log(1 - successProbs->at(k));
                                                   ˜˜˜˜˜     ^
cstat.cpp:2631:92: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      for (int k=0; k < nsuccessProbs; k++) ans += nvars->at(k) * log(1 - successProbs->at(k));
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜     ^
cstat.cpp:2640:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          tmp += exp( log((double) nvars->at(k)) + (i+.0) * (log(successProbs->at(k)) - log(1- successProbs->at(k))) );
                                   ˜˜˜˜˜     ^
cstat.cpp:2640:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          tmp += exp( log((double) nvars->at(k)) + (i+.0) * (log(successProbs->at(k)) - log(1- successProbs->at(k))) );
                                                                 ˜˜˜˜˜˜˜˜˜˜˜˜     ^
cstat.cpp:2640:106: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          tmp += exp( log((double) nvars->at(k)) + (i+.0) * (log(successProbs->at(k)) - log(1- successProbs->at(k))) );
                                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜     ^
cstat.cpp:2646:85: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        tmp= dpoissonbin(x-i, successProbs, nvars, 0, Tvector, poibinProbs) * Tvector->at(i-1);
                                                                              ˜˜˜˜˜˜˜     ˜^˜
cstat.cpp:2655:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        for (i=0; i<nsuccessProbs; i++) mu += successProbs->at(i);
                                              ˜˜˜˜˜˜˜˜˜˜˜˜     ^
cstat.cpp:2656:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ans = min( dpoisson(x, mu, 1), poibinProbs->at(x-1)); //avoid overflow: previous value / Poisson approx (law of small numbers)
                                       ˜˜˜˜˜˜˜˜˜˜˜     ˜^˜
cstat.cpp:2624:21: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int npoibinProbs= poibinProbs->size(), nsuccessProbs= successProbs->size(); 
      ˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.cpp:2624:57: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int npoibinProbs= poibinProbs->size(), nsuccessProbs= successProbs->size(); 
                                         ˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cstat.cpp:2637:31: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
      for (i= Tvector->size() +1; i <= x; i++) {
            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
22 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c dataframe.cpp -o dataframe.o
dataframe.cpp:70:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        e->num = this->exons.size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c discretedf.cpp -o discretedf.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c exon.cpp -o exon.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fragFunc.c -o fragFunc.o
fragFunc.c:19:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    frags[pos].exons=malloc((exonNum+1) * sizeof(int));
                             ˜˜˜˜˜˜˜^˜  ˜
fragFunc.c:20:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    frags[pos].starts=malloc((exonNum+1) * sizeof(int));
                              ˜˜˜˜˜˜˜^˜  ˜
fragFunc.c:21:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    frags[pos].rids=malloc((exonNum+1) * sizeof(int));  
                            ˜˜˜˜˜˜˜^˜  ˜
fragFunc.c:25:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        newexons = realloc(frags[pos].exons, (frags[pos].nexon + exonNum) * sizeof(int));
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜  ˜
fragFunc.c:28:57: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        newstarts=realloc(frags[pos].starts, (frags[pos].nexon + exonNum) * sizeof(int));
                                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜  ˜
fragFunc.c:31:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        newrids=realloc(frags[pos].rids, (frags[pos].nexon + exonNum) * sizeof(int));
                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜  ˜
fragFunc.c:46:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  *frags = malloc((totFnow + 1) * sizeof(path_t));
                   ˜˜˜˜˜˜˜˜^˜˜  ˜
fragFunc.c:59:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        newF= realloc(*frags, totFnow * sizeof(path_t));
                              ^˜˜˜˜˜˜ ˜
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 fragment.cpp -o fragment.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c functions.c -o functions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c hash.c -o hash.o
hash.c:77:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  tptr->bucket=(hash_node_t **) calloc(tptr->size, sizeof(hash_node_t *));
                                ˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜
hash.c:197:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  char *ns=(char*)malloc(l*sizeof(char));
                         ^˜
hash.c:196:18: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  int l=strlen(o)+1;
      ˜ ˜˜˜˜˜˜˜˜˜^˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c join_exons.c -o join_exons.o
join_exons.c:35:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  links=malloc((tot+1) * sizeof(int *));
                ˜˜˜^˜  ˜
join_exons.c:46:74: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      if(links[l][0] % 49 == 0) links[l] = realloc(links[l], (links[l][0]+50) * sizeof(int)); 
                                                              ˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
join_exons.c:60:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  ans = malloc((counter+1) * sizeof(char *));
                ˜˜˜˜˜˜˜^˜  ˜
join_exons.c:66:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      qsort(&links[i][1], links[i][0], sizeof(int), compare);
      ˜˜˜˜˜               ^˜˜˜˜˜˜˜˜˜˜
join_exons.c:70:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        ans[j] = malloc(15 * (links[i][0]+1) * sizeof(char));
                        ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
join_exons.c:91:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  tmpcounts = malloc(finalSize * sizeof(int));
                     ^˜˜˜˜˜˜˜˜ ˜
join_exons.c:93:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  tmpkey = malloc(finalSize * sizeof(char *));
                  ^˜˜˜˜˜˜˜˜ ˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c makeIslands.c -o makeIslands.o
makeIslands.c:148:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  ex2tx = malloc((totExo*2) * sizeof(int *));
                  ˜˜˜˜˜˜^˜  ˜
makeIslands.c:149:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  tx2ex = malloc((totExo*2) * sizeof(int *));
                  ˜˜˜˜˜˜^˜  ˜
makeIslands.c:161:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
       ex2tx[l] = malloc((p_tab[i]+2) * sizeof(int));
                          ˜˜˜˜˜˜˜˜^˜  ˜
makeIslands.c:169:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
       tx2ex[l] = malloc((p_tabtx[i]+2) * sizeof(int));
                          ˜˜˜˜˜˜˜˜˜˜^˜  ˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c model.cpp -o model.o
model.cpp:22:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int i = this->items.size();
                    ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
model.cpp:48:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int i = this->items.size();
                    ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
model.cpp:74:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int i = this->items.size();
                    ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
model.cpp:102:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        return this->items.size();
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
model.cpp:110:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return this->items.at(i);
               ˜˜˜˜           ^
model.cpp:252:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (this->contains(allvariants->at(i)))
                                   ˜˜˜˜˜˜˜˜˜˜˜     ^
model.cpp:240:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int n = allvariants->size();
            ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c model_cmp.cpp -o model_cmp.o
model_cmp.cpp:11:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        return va->hashcode;
        ˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c pathCounts.c -o pathCounts.o
pathCounts.c:26:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    hashSize=pow(2,25); 
            ˜^˜˜˜˜˜˜˜˜
pathCounts.c:100:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    ord=malloc((frags[pos].nexon+1) * sizeof(int));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
pathCounts.c:101:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    unex=malloc((frags[pos].nexon+1) * sizeof(int));
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
pathCounts.c:102:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    unrid=malloc((frags[pos].nexon+1) * sizeof(int));
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
pathCounts.c:103:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    standex=malloc((frags[pos].nexon+1) * sizeof(int *));
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
pathCounts.c:112:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(standex, frags[pos].nexon, sizeof(int **), sort);
    ˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
pathCounts.c:139:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    pastr=malloc((totEx+1)*50 * sizeof(char));
                 ˜˜˜˜˜˜˜˜˜^˜˜ ˜
pathCounts.c:143:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    lread=malloc((totEx+1) * sizeof(int));
                  ˜˜˜˜˜^˜  ˜
pathCounts.c:144:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    rread=malloc((totEx+1) * sizeof(int));
                  ˜˜˜˜˜^˜  ˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c procBam.c -o procBam.o
procBam.c:23:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        frags = malloc((frags_size[0] + 1) * sizeof(read_t));
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜  ˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rcasper.cpp -o rcasper.o
rcasper.cpp:93:32: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
      for (int l = strlen(left)-1; l >= 0; l--) { if (left[l] == '.') leftc++; }  
               ˜   ˜˜˜˜˜˜˜˜˜˜˜˜^˜
rcasper.cpp:95:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
      for (int r = strlen(right)-1; r >= 0; r--) { if (right[r] == '.') rightc++; } 
               ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
rcasper.cpp:310:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                v->name= string(CHAR(STRING_ELT(tnames, i)), nbchar);
                         ˜˜˜˜˜˜                              ^˜˜˜˜˜
rcasper.cpp:482:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int np = (casp->frame->data).size();
        ˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
rcasper.cpp:965:34: warning: '&&' within '||' [-Wlogical-op-parentheses]
                if (method == 1 || method == 0 && df->exons.size() <= 4) 
                                ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
rcasper.cpp:965:34: note: place parentheses around the '&&' expression to silence this warning
                if (method == 1 || method == 0 && df->exons.size() <= 4) 
                                               ^
                                   (                                   )
rcasper.cpp:1087:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                if (selBest==0) { nx= resProbs.size(); } else { nx=1; }
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c seppel.cpp -o seppel.o
seppel.cpp:93:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i=0; i< imax; i++) priorpNbVars[i] -= psum;
                              ˜˜˜˜˜˜˜˜˜˜˜˜ ^
seppel.cpp:35:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int E= frame->exons.size();
      ˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
seppel.cpp:379:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        Model* omodl = possiblemodels->at(onum);
                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^˜˜˜
seppel.cpp:395:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                Model* nmodl = possiblemodels->at(nnum);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜     ^˜˜˜
seppel.cpp:377:49: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        int onum = runifdisc(0, possiblemodels->size() - 1);
                   ˜˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
seppel.cpp:393:50: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
                int nnum = runifdisc(0, possiblemodels->size() - 1);
                           ˜˜˜˜˜˜˜˜˜    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
seppel.cpp:745:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      ans= priorpNbVars[nbVars-1];
           ˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
seppel.cpp:759:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          Sk[v->exonCount -1]++;
          ˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
seppel.cpp:763:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        vector<int> Fk (E);
                    ˜˜  ^
seppel.cpp:765:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        for (int i=0; i< E; i++) Fk[i]= nvarsPoibin[i] - Sk[i];
                                 ˜˜ ^
seppel.cpp:765:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        for (int i=0; i< E; i++) Fk[i]= nvarsPoibin[i] - Sk[i];
                                        ˜˜˜˜˜˜˜˜˜˜˜ ^
seppel.cpp:765:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        for (int i=0; i< E; i++) Fk[i]= nvarsPoibin[i] - Sk[i];
                                                         ˜˜ ^
seppel.cpp:771:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          ans += Sk[i] * log(priorpNbExons[i]) + Fk[i] * log(1-priorpNbExons[i]);
                 ˜˜ ^
seppel.cpp:771:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          ans += Sk[i] * log(priorpNbExons[i]) + Fk[i] * log(1-priorpNbExons[i]);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
seppel.cpp:771:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          ans += Sk[i] * log(priorpNbExons[i]) + Fk[i] * log(1-priorpNbExons[i]);
                                                 ˜˜ ^
seppel.cpp:771:78: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          ans += Sk[i] * log(priorpNbExons[i]) + Fk[i] * log(1-priorpNbExons[i]);
                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
seppel.cpp:733:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int E= frame->exons.size(), nbVars= model->count();
        ˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
17 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c simReads.c -o simReads.o
simReads.c:62:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  genes = malloc((ngenes+1) * sizeof(gene_t));
                  ˜˜˜˜˜˜^˜  ˜
simReads.c:67:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  srand(seed);
  ˜˜˜˜˜ ^˜˜˜
simReads.c:114:20: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  hash_init(paths, NextPow2(n)); 
  ˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜
simReads.c:114:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  hash_init(paths, NextPow2(n)); 
                   ˜˜˜˜˜˜˜˜ ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c simReadsfunc.c -o simReadsfunc.o
simReadsfunc.c:18:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    genes[i].vars = malloc((vn[i]+1) * sizeof(var_t));
                            ˜˜˜˜˜^˜  ˜
simReadsfunc.c:24:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      genes[i].vars[j].exst = malloc((genes[i].vars[j].nex+1) * sizeof(int));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
simReadsfunc.c:25:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      genes[i].vars[j].exst = malloc((genes[i].vars[j].nex+1) * sizeof(int));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
simReadsfunc.c:26:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      genes[i].vars[j].exen = malloc((genes[i].vars[j].nex+1) * sizeof(int));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
simReadsfunc.c:27:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      genes[i].vars[j].exid = malloc((genes[i].vars[j].nex+1) * sizeof(int));
                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜  ˜
simReadsfunc.c:156:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  pa = malloc((40 * var.nex) * sizeof(char));
               ˜˜˜^˜˜˜˜˜˜˜˜  ˜
simReadsfunc.c:164:71: warning: variable 'en' is uninitialized when used here [-Wuninitialized]
    if((var.len - st - len + 2)<0) Rprintf("%d %d %d %d %d %d\n", st, en, rst, ren, var.len, len);    
                                                                      ^˜
simReadsfunc.c:152:9: note: initialize the variable 'en' to silence this warning
  int en, rst, ren, wis, sum;
        ^
         = 0
simReadsfunc.c:164:80: warning: variable 'ren' is uninitialized when used here [-Wuninitialized]
    if((var.len - st - len + 2)<0) Rprintf("%d %d %d %d %d %d\n", st, en, rst, ren, var.len, len);    
                                                                               ^˜˜
simReadsfunc.c:152:19: note: initialize the variable 'ren' to silence this warning
  int en, rst, ren, wis, sum;
                  ^
                   = 0
simReadsfunc.c:164:75: warning: variable 'rst' is uninitialized when used here [-Wuninitialized]
    if((var.len - st - len + 2)<0) Rprintf("%d %d %d %d %d %d\n", st, en, rst, ren, var.len, len);    
                                                                          ^˜˜
simReadsfunc.c:152:14: note: initialize the variable 'rst' to silence this warning
  int en, rst, ren, wis, sum;
             ^
              = 0
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c smartmodeldist.cpp -o smartmodeldist.o
smartmodeldist.cpp:135:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        Exon* e = frame->exons[ei];
                                  ˜˜˜˜˜        ^˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c uniqQname.c -o uniqQname.o
uniqQname.c:29:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
  tmpres = malloc(floor(totReads/2) * sizeof(char*));
           ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c variant.cpp -o variant.o
variant.cpp:19:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        this->exonCount = exons->size();
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c variant_cmp.cpp -o variant_cmp.o
variant_cmp.cpp:11:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        return va->hashcode;
        ˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜
1 warning 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 casper.so casper.o cstat.o dataframe.o discretedf.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/casper.Rcheck/casper/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
Creating a generic function for 'plot' from package 'graphics' in package 'casper'
Creating a generic function for 'lines' from package 'graphics' in package 'casper'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (casper)

casper.Rcheck/casper-Ex.timings:

nameusersystemelapsed
K562.r1l10.3470.0180.376
annotatedGenome-class0.0090.0060.014
calcExp10.882 1.00012.273
genePlot2.3440.0302.414
getDistrs2.5510.0592.845
getIsland0.1950.0130.233
getNreads0.0310.0040.035
getReads0.0020.0030.005
hg19DB0.1700.0100.277
mergeExp0.0020.0040.006
pathCounts-class0.0210.0030.026
pathCounts0.0220.0050.027
plot-methods0.0210.0020.025
procBam-class0.0280.0040.034
procBam0.0250.0060.030
procGenome0.6850.0090.707
rmShortInserts0.0030.0050.008
simReads2.5430.0622.631
transcripts1.0580.0151.093
wrapKnown0.0240.0060.030