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 |
* 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)