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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD INSTALL DECIPHER
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* installing to library ‘/home/biocbuild/bbs-3.6-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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] = {
^
CalculateFISH.c:25:23: note: (near initialization for ‘dH_DR’)
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DR[4][4] = {
^
CalculateFISH.c:31:23: note: (near initialization for ‘dS_DR’)
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_DD[4][4] = {
^
CalculateFISH.c:37:23: note: (near initialization for ‘dH_DD’)
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_DD[4][4] = {
^
CalculateFISH.c:43:23: note: (near initialization for ‘dS_DD’)
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
double dH_RR[4][4] = {
^
CalculateFISH.c:49:23: note: (near initialization for ‘dH_RR’)
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
double dS_RR[4][4] = {
^
CalculateFISH.c:55:23: note: (near initialization for ‘dS_RR’)
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:281:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minCol = minC;
^
ClusterNJ.c:195:62: note: ‘minC’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
^
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minRow = minR;
^
ClusterNJ.c:195:56: note: ‘minR’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
^
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:40:0,
from ClusterNJ.c:11:
ClusterNJ.c: In function ‘clusterNJ’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
ClusterNJ.c:198:29: note: ‘utilsPackage’ was declared here
SEXP ans, percentComplete, utilsPackage;
^
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:40:0,
from ClusterNJ.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
ClusterNJ.c:198:12: note: ‘percentComplete’ was declared here
SEXP ans, percentComplete, utilsPackage;
^
ClusterNJ.c:487:24: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*rPercentComplete = floor(100*soFar/total);
^
ClusterNJ.c:492:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:200:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minCol = minC;
^
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
^
ClusterUPGMA.c:199:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
minRow = minR;
^
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
^
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:40:0,
from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function ‘clusterUPGMA’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
ClusterUPGMA.c:127:29: note: ‘utilsPackage’ was declared here
SEXP ans, percentComplete, utilsPackage;
^
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:40:0,
from ClusterUPGMA.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
ClusterUPGMA.c:127:12: note: ‘percentComplete’ was declared here
SEXP ans, percentComplete, utilsPackage;
^
ClusterUPGMA.c:426:24: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*rPercentComplete = floor(100*soFar/total);
^
ClusterUPGMA.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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:975:11: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c] = (k - 1) & 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:1164:14: 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:626:25: warning: ‘lastCase’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int run, lastTriplet, lastCase;
^
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:1054:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
^
Compression.c:539:17: note: ‘dict’ was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int do_HEC, n, l, d;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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] = {
^
DesignProbes.c:70:20: note: (near initialization for ‘NN’)
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
double PM[4][4] = {
^
DesignProbes.c:77:20: note: (near initialization for ‘PM’)
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
double sMM[4][5][5][4] = {
^
DesignProbes.c:84:27: note: (near initialization for ‘sMM’)
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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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;
^
EnumerateSequence.c: In function ‘enumerateGappedSequence’:
EnumerateSequence.c:277:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
^
EnumerateSequence.c: In function ‘enumerateGappedSequenceAA’:
EnumerateSequence.c:400:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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] = {
^
MeltPolymer.c:79:20: note: (near initialization for ‘dH’)
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
double dS[4][4] = {
^
MeltPolymer.c:88:20: note: (near initialization for ‘dS’)
MeltPolymer.c:373:33: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
slope = (*(rans + stack[0] + l*s) - *(rans + stack[pos] + l*s))/(t[stack[0]] - t[stack[pos]]);
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:453:24: note: ‘utilsPackage’ was declared here
SEXP percentComplete, utilsPackage;
^
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:453:7: note: ‘percentComplete’ was declared here
SEXP percentComplete, utilsPackage;
^
MultiMatch.c:547:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include/Rdefines.h:40:0,
from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include/Rdefines.h:40:0,
from NNLS.c:11:
/home/biocbuild/bbs-3.6-bioc/R/include/Rinternals.h:1222:16: 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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/include/Rdefines.h:37:0,
from PredictDBN.c:11:
PredictDBN.c: In function ‘predictDBN’:
/home/biocbuild/bbs-3.6-bioc/R/include/R_ext/RS.h:74:25: warning: ‘MI2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
^
PredictDBN.c:399:10: note: ‘MI2’ was declared here
double *MI2, *rowMax, *colMax;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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:246:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
*(rans + 3*j + 2) = C/sum;
^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.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 TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/R/library/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
* DONE (DECIPHER)
