##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:401:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lGp *= tot;
˜˜˜˜^˜˜˜˜˜
AlignProfiles.c:39:39: note: ‘lGp’ was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
^˜˜
AlignProfiles.c:403:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lGs *= tot;
˜˜˜˜^˜˜˜˜˜
AlignProfiles.c:39:44: note: ‘lGs’ was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
^˜˜
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.1’:
AlignProfiles.c:1220:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lGp *= tot;
˜˜˜˜^˜˜˜˜˜
AlignProfiles.c:763:39: note: ‘lGp’ was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
^˜˜
AlignProfiles.c:1222:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lGs *= tot;
˜˜˜˜^˜˜˜˜˜
AlignProfiles.c:763:44: note: ‘lGs’ was declared here
double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
^˜˜
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:355:11: warning: ‘Ps’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
^˜˜
AlignProfiles.c:355:11: warning: ‘Pp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘Os’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘Op’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_DR[4][4] = {
^
-11.5, -7.8, -7, -8.3,
{ }
-10.4, -12.8, -16.3, -9.1,
{ }
-8.6, -8, -9.3, -5.9,
{ }
-7.8, -5.5, -9, -7.8
{
};
}
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DR[4][4] = {
^
-36.4, -21.6, -19.7, -23.9,
{ }
-28.4, -31.9, -47.1, -23.5,
{ }
-22.9, -17.1, -23.2, -12.3,
{ }
-23.2, -13.5, -26.1, -21.9
{
};
}
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_DD[4][4] = {
^
-7.9, -8.4, -7.8, -7.2,
{ }
-8.5, -8, -10.6, -7.8,
{ }
-8.2, -9.8, -8, -8.4,
{ }
-7.2, -8.2, -8.5, -7.9
{
};
}
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DD[4][4] = {
^
-22.2, -22.4, -21, -20.4,
{ }
-22.7, -19.9, -27.2, -21,
{ }
-22.2, -24.4, -19.9, -22.4,
{ }
-21.3, -22.2, -22.7, -22.2
{
};
}
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_RR[4][4] = {
^
-6.6, -10.17, -7.65, -5.76,
{ }
-10.56, -12.21, -7.95, -7.65,
{ }
-13.37, -14.21, -12.21, -10.17,
{ }
-8.11, -13.37, -10.56, -6.6
{
};
}
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_RR[4][4] = {
^
-18.38, -26.03, -19.18, -15.67,
{ }
-28.25, -30.02, -19.18, -19.18,
{ }
-35.68, -34.85, -30.02, -26.03,
{ }
-22.59, -35.68, -28.25, -18.38
{
};
}
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:414:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^˜˜
ChainSegments.c:414:67: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:403:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minCol = minC;
˜˜˜˜˜˜˜^˜˜˜˜˜
Cluster.c:229:50: note: ‘minC’ was declared here
int k, dobj, clusterNum, minRow, minCol, index, minC, met;
^˜˜˜
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:418:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minCols[rowIndices[i]] = minC;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
Cluster.c:229:50: note: ‘minC’ was declared here
int k, dobj, clusterNum, minRow, minCol, index, minC, met;
^˜˜˜
Cluster.c: In function ‘cluster’:
Cluster.c:229:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:451:168: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
rans[4*(length - 1) + k] = dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[minRow] - colIndices[minCol]]/2 + (nDiv[minCol] - nDiv[minRow + 1])/(2*(size-2)); // col
^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:973:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c] = ((k - 1) >> 8) & 0xFF; // length of run
˜˜˜^˜˜˜
Compression.c:513:12: note: ‘k’ was declared here
int i, j, k, pos;
^
Compression.c:1007:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
count++;
˜˜˜˜˜^˜
Compression.c:539:29: note: ‘count’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^˜˜˜˜
Compression.c:1006:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
word = (word << 8) | (unsigned int)reorder(byte);
˜˜˜˜˜˜^˜˜˜˜
Compression.c:539:23: note: ‘word’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^˜˜˜
Compression.c:1209:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = rev==0 ? 254 : 255;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Compression.c:540:27: note: ‘rev’ was declared here
int lastTemp, currTemp, rev, len, len2, thresh = 1;
^˜˜
Compression.c:553:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int lower = 0;
^˜˜˜˜
Compression.c:1236:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Compression.c:626:12: note: ‘lastTriplet’ was declared here
int run, lastTriplet, lastCase;
^˜˜˜˜˜˜˜˜˜˜
Compression.c:1026:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[(word >> k) & 0xFF];
^
Compression.c:539:17: note: ‘dict’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *DBN, *s;
^˜˜
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(runs + s) += weight;
^˜
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
^˜˜˜˜˜˜
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *HEC, *s;
^˜˜
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1938:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_DBN, n, l, d;
^
ConsensusSequence.c:1937:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *DBN, *s;
^˜˜
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_HEC, n, l, d;
^
ConsensusSequence.c:2062:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double *HEC, *s;
^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
double NN[4][4] = {
^
-0.816507461,-2.5401714,-1.647430026,-1.184658548
{
,-1.854740485,-2.479102613,-2.826248182,-1.647430026
}{
,-2.48761723,-4.694133177,-2.479102613,-2.5401714
}{
,-0.495794417,-2.48761723,-1.854740485,-0.816507461
}{
};
}
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
double PM[4][4] = {
^
-0.141370102,-0.439805276,-0.285236035,-0.205111781
{
,-0.321129768,-0.429231826,-0.48933661,-0.285236035
}{
,-0.430706047,-0.812742218,-0.429231826,-0.439805276
}{
,-0.085841845,-0.430706047,-0.321129768,-0.141370102
}{
};
}
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
double sMM[4][5][5][4] = {
^
0,0,0,0
{
{
{
,1.545032445,1.254355018,1.491691514,1.329138183
}{
,1.150635633,0.582415494,1.075877275,1.187937642
}{
,1.203555051,1.001540513,0.864287715,0.717125848
}{
,0.75,0.65,0.69,0.78
}{
,0.630005348,0.18553379,0.730763505,0.709272397
}
}{
{
,0,0,0,0
}{
,0.856582783,-0.143236405,0.716721488,0.603652831
}{
,0.851622883,0.653168672,0.676545316,1.187937642
}{
,0.75,0.65,0.69,0.78
}{
,1.231861002,0.746214538,1.087821916,0.989140748
}
}{
{
,1.822113278,1.270687029,1.336192565,1.364584949
}{
,0,0,0,0
}{
,1.443665704,1.385046493,1.256013166,1.329138183
}{
,0.75,0.65,0.69,0.78
}{
,1.478009492,0.882097231,1.20450984,1.061002478
}
}{
{
,1.496720812,0.846496194,0.967868114,0.989140748
}{
,0.766581547,-0.024857805,0.50754303,0.709272397
}{
,0,0,0,0
}{
,0.75,0.65,0.69,0.78
}{
,0.75,0.65,0.69,0.78
}
}{
{
,0.75,0.65,0.69,0.78
}{
,0.75,0.65,0.69,0.78
}{
,0.76,0.65,0.69,0.78
}{
,0,0,0,0
}{
,0,0,0,0
}
}
}{
{
{
,1.295827995,0.84547091,0.91019099,1.256013166
}{
,0.755889609,0.241428373,0.396379912,0.676545316
}{
,0.99945386,0.740323132,0.435659206,0.864287715
}{
,0.65,0.55,0.48,0.69
}{
,0.843147406,0.101248351,0.49063599,0.50754303
}
}{
{
,0,0,0,0
}{
,1.0651638,0.249934344,0.699352949,0.716721488
}{
,0.871921533,0.59458138,0.396379912,1.075877275
}{
,0.65,0.56,0.49,0.69
}{
,1.07531714,0.318907854,0.653287717,0.967868114
}
}{
{
,1.099899195,0.730184613,0.661798984,1.336192565
}{
,0,0,0,0
}{
,1.45897431,1.318532145,0.91019099,1.491691514
}{
,0.65,0.56,0.49,0.69
}{
,1.242135174,0.894838095,1.108555445,1.20450984
}
}{
{
,0.911428974,0.524430101,0.653287717,1.087821916
}{
,0.503209827,0.274849491,0.49063599,0.730763505
}{
,0,0,0,0
}{
,0.65,0.55,0.48,0.69
}{
,0.65,0.55,0.48,0.69
}
}{
{
,0.65,0.56,0.49,0.69
}{
,0.65,0.56,0.49,0.69
}{
,0.65,0.55,0.48,0.69
}{
,0,0,0,0
}{
,0,0,0,0
}
}
}{
{
{
,1.100661785,0.969784756,1.318532145,1.385046493
}{
,0.565895968,-0.060347902,0.59458138,0.653168672
}{
,0.782168488,0.788161238,0.740323132,1.001540513
}{
,0.68,0.46,0.55,0.65
}{
,0.468913405,-0.469855984,0.274849491,-0.024857805
}
}{
{
,0,0,0,0
}{
,0.258195131,-0.70438632,0.249934344,-0.143236405
}{
,0.502914193,-0.060347902,0.241428373,0.582415494
}{
,0.68,0.47,0.56,0.65
}{
,0.584083861,0.258975454,0.524430101,0.846496194
}
}{
{
,0.968040559,0.797499702,0.730184613,1.270687029
}{
,0,0,0,0
}{
,1.081040749,0.969784756,0.84547091,1.254355018
}{
,0.68,0.47,0.56,0.65
}{
,1.048553951,0.728354541,0.894838095,0.882097231
}
}{
{
,0.88611252,0.258975454,0.318907854,0.746214538
}{
,0.239520858,-0.469855984,0.101248351,0.18553379
}{
,0,0,0,0
}{
,0.68,0.46,0.55,0.65
}{
,0.68,0.46,0.55,0.65
}
}{
{
,0.68,0.47,0.56,0.65
}{
,0.68,0.47,0.56,0.65
}{
,0.68,0.46,0.55,0.65
}{
,0,0,0,0
}{
,0,0,0,0
}
}
}{
{
{
,1.566899704,1.081040749,1.45897431,1.443665704
}{
,0.976725675,0.502914193,0.871921533,0.851622883
}{
,1.482046826,0.782168488,0.99945386,1.203555051
}{
,0.85,0.68,0.65,0.76
}{
,0.798628781,0.239520858,0.503209827,0.766581547
}
}{
{
,0,0,0,0
}{
,1.141098246,0.258195131,1.0651638,0.856582783
}{
,0.976725675,0.565895968,0.755889609,1.150635633
}{
,0.85,0.68,0.65,0.75
}{
,1.125403302,0.88611252,0.911428974,1.496720812
}
}{
{
,1.68169282,0.968040559,1.099899195,1.822113278
}{
,0,0,0,0
}{
,1.566899704,1.100661785,1.295827995,1.545032445
}{
,0.85,0.68,0.65,0.75
}{
,1.35948517,1.048553951,1.242135174,1.478009492
}
}{
{
,1.125403302,0.584083861,1.07531714,1.231861002
}{
,0.798628781,0.468913405,0.843147406,0.630005348
}{
,0,0,0,0
}{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
}
}{
{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
}{
,0.85,0.68,0.65,0.75
}{
,0,0,0,0
}{
};
}
}
}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^˜˜˜˜˜˜˜˜
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cycles += lastCycle - thisCycle;
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
^˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:625:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if (!ci)
^˜
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
while (i < ex) {
^˜˜˜˜
DistanceMatrix.c:647:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if (!cj)
^˜
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
while (j < ey) {
^˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:268:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
x = x + (x >> 4) & 0xF0F0F0F;
˜˜^˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:376:7: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (k==1) {
^
FindFrameshifts.c:372:8: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
j -= B[k*rc + j*r + i];
˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FindFrameshifts.c:318:22: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (C[k*rc + j*r + i] >= 0) {
˜˜˜˜˜˜˜˜˜˜˜^˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
double dH[4][4] = {
^
-7.9,-8.4,-7.8,-7.2
{
,-8.5,-8.0,-10.6,-7.8
}{
,-8.2,-9.8,-8.0,-8.4
}{
,-7.2,-8.2,-8.5,-7.9
}{
};
}
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
double dS[4][4] = {
^
-22.2,-22.4,-21.0,-20.4
{
,-22.7,-19.9,-27.2,-21.0
}{
,-22.2,-24.4,-19.9,-22.4
}{
,-21.3,-22.2,-22.7,-22.2
}{
};
}
MeltPolymer.c:339:16: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(rans + k + (seq_length - 1)*l) = V_10_LR[seq_length]/Q_tot;
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MultiMatch.c -o MultiMatch.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:244:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:244:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MultiMatch.c:327:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:352:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:352:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MultiMatch.c:428:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:454:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
MultiMatch.c:454:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MultiMatch.c:543:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
NNLS.c:47:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
from NNLS.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^˜˜˜˜˜˜
NNLS.c:47:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
NNLS.c:82:13: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:833:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]] + 1;
^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ret, i, ans);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PredictHEC.c:42:8: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
char *states;
^˜˜˜˜˜
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
double H, E, C, sum, *rans;
^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)
