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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DECIPHER_2.22.0.tar.gz && rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DECIPHER_2.22.0.zip && rm DECIPHER_2.22.0.tar.gz DECIPHER_2.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 10.8M 0 59186 0 0 223k 0 0:00:49 --:--:-- 0:00:49 224k
6 10.8M 6 713k 0 0 552k 0 0:00:20 0:00:01 0:00:19 552k
15 10.8M 15 1737k 0 0 758k 0 0:00:14 0:00:02 0:00:12 758k
32 10.8M 32 3638k 0 0 1116k 0 0:00:09 0:00:03 0:00:06 1116k
58 10.8M 58 6505k 0 0 1528k 0 0:00:07 0:00:04 0:00:03 1527k
92 10.8M 92 10.0M 0 0 1957k 0 0:00:05 0:00:05 --:--:-- 2047k
100 10.8M 100 10.8M 0 0 2039k 0 0:00:05 0:00:05 --:--:-- 2501k
install for i386
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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: 'subM' 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)
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:375:26: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
CalculateDeltaG.c:375:22: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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
{
};
}
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:422:72: 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:422:67: warning: 'upX' may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:766:19: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
nDiv[minCol] -= dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[j] - colIndices[minCol]]; // col sums
^~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
^~
ClusterML.c:420:6: note: 'count' was declared here
int count;
^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
#pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (k==1 && letter >= 11) {
^
Compression.c:516:12: note: 'k' was declared here
int i, j, k, pos;
^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
count++;
~~~~~^~
Compression.c:542:29: note: 'count' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
word = (word << 8) | (unsigned int)reorder(byte);
~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
Compression.c:1167:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = rev==0 ? 254 : 255;
~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
int lastTemp, currTemp, rev, len, len2, thresh = 1;
^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lower = 0;
^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
int run, lastTriplet, lastCase;
^~~~~~~~~~~
Compression.c:1057:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
^
Compression.c:542:17: note: 'dict' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:456:14: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
} else if (length==2) { // run of length 3
^
ConsensusSequence.c:397:15: note: 'length' was declared here
int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
^~~~~~
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;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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) {
^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
x = x + (x >> 4) & 0xF0F0F0F;
~~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
pos = i*3 + k + 1;
~^~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:388:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c:432:29: warning: 'lastVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += codons[lastVal*64 + val];
~~~~~~~^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:793:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:894:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:928:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1031:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1092:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1188:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1286:21: warning: 'x_i.length' may be used uninitialized in this function [-Wmaybe-uninitialized]
(s==0 && j >= 0 && j + w <= x_i.length)) {
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1350:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1461:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1573:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1681:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1788:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1882:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1950:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2057:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2276:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2421:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2522:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2554:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *rans;
^~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:866:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
int i, j, k, temp, start = 0;
^~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rdefines.h:42,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rinternals.h:1557:16: 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 C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rdefines.h:42,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rinternals.h:1557:16: 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;
~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:869:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]];// + 1;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:231:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
states[j] = 'E';
~~~~~~~~~~^~~~~
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double H, E, C, sum, *rans;
^~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def 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 GeneFinding.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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DECIPHER.buildbin-libdir/00LOCK-DECIPHER/00new/DECIPHER/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DECIPHER'
finding HTML links ... done
AA_REDUCED html
Add2DB html
AdjustAlignment html
AlignDB html
AlignProfiles html
AlignSeqs html
AlignSynteny html
AlignTranslation html
AmplifyDNA html
Array2Matrix html
BrowseDB html
BrowseSeqs html
CalculateEfficiencyArray html
CalculateEfficiencyFISH html
CalculateEfficiencyPCR html
Codec html
ConsensusSequence html
Cophenetic html
CorrectFrameshifts html
CreateChimeras html
DB2Seqs html
DECIPHER-package html
DesignArray html
DesignPrimers html
DesignProbes html
DesignSignatures html
DetectRepeats html
DigestDNA html
Disambiguate html
DistanceMatrix html
ExtractGenes html
FindChimeras html
FindGenes html
FindNonCoding html
FindSynteny html
FormGroups html
Genes-class html
HEC_MI html
IdClusters html
IdConsensus html
IdLengths html
IdTaxa html
IdentifyByRank html
LearnNonCoding html
LearnTaxa html
MIQS html
MODELS html
MapCharacters html
MaskAlignment html
MeltDNA html
NNLS html
NonCoding-class html
NonCodingRNA html
OrientNucleotides html
PFASUM html
PredictDBN html
PredictHEC html
RESTRICTION_ENZYMES html
ReadDendrogram html
RemoveGaps html
SearchDB html
Seqs2DB html
StaggerAlignment html
Synteny-class html
Taxa-class html
TerminalChar html
TileSeqs html
TrainingSet_16S html
TrimDNA html
WriteDendrogram html
WriteGenes html
deltaGrules html
deltaHrules html
deltaHrulesRNA html
deltaSrules html
deltaSrulesRNA html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'DECIPHER' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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: 'subM' 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)
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:375:26: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
CalculateDeltaG.c:375:22: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i, j, k, count, s1, s2;
^~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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
{
};
}
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:422:72: 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:422:67: warning: 'upX' may be used uninitialized in this function [-Wmaybe-uninitialized]
int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
^~
ClusterML.c:420:6: note: 'count' was declared here
int count;
^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
#pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (k==1 && letter >= 11) {
^
Compression.c:516:12: note: 'k' was declared here
int i, j, k, pos;
^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
count++;
~~~~~^~
Compression.c:542:29: note: 'count' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
word = (word << 8) | (unsigned int)reorder(byte);
~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
Compression.c:1212:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = rev==0 ? 254 : 255;
~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
int lastTemp, currTemp, rev, len, len2, thresh = 1;
^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
int lower = 0;
^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
int run, lastTriplet, lastCase;
^~~~~~~~~~~
Compression.c:1029:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
lastHit = dict[(word >> k) & 0xFF];
^
Compression.c:542:17: note: 'dict' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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) {
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
x = x + (x >> 4) & 0xF0F0F0F;
~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
pos = i*3 + k + 1;
~^~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:388:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c:432:29: warning: 'lastVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
score += codons[lastVal*64 + val];
~~~~~~~^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:793:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:894:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:928:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1031:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1092:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1188:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1286:21: warning: 'x_i.length' may be used uninitialized in this function [-Wmaybe-uninitialized]
(s==0 && j >= 0 && j + w <= x_i.length)) {
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1350:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1461:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1573:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1681:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1788:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1882:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1990:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
^
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2090:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
^
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2276:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2421:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2522:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
val += 16*getBaseRC(x_i.ptr[j]);
^
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2554:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Chars_holder x_i;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double *rans;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:866:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
int i, j, k, temp, start = 0;
^~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rdefines.h:42,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rinternals.h:1557:16: 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 C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rdefines.h:42,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rinternals.h:1557:16: 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;
~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:869:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]];// + 1;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def 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 GeneFinding.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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.22.0.zip
* DONE (DECIPHER)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DECIPHER' successfully unpacked and MD5 sums checked
