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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DECIPHER_2.14.0.tar.gz && rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DECIPHER_2.14.0.zip && rm DECIPHER_2.14.0.tar.gz DECIPHER_2.14.0.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
100 8882k 100 8882k 0 0 60.9M 0 --:--:-- --:--:-- --:--:-- 62.8M
install for i386
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
-11.5, -7.8, -7, -8.3,
^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
-36.4, -21.6, -19.7, -23.9,
^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9, -8.4, -7.8, -7.2,
^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2, -22.4, -21, -20.4,
^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
-6.6, -10.17, -7.65, -5.76,
^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
-18.38, -26.03, -19.18, -15.67,
^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:420:72: 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:420:67: 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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k, dobj, clusterNum, minRow, minCol, index, minC, met;
^
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from Cluster.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
Cluster.c:233:29: note: 'utilsPackage' was declared here
SEXP ans, percentComplete, utilsPackage;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from Cluster.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
Cluster.c:233:12: note: 'percentComplete' was declared here
SEXP ans, percentComplete, utilsPackage;
^
Cluster.c:789:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
*rPercentComplete = floor(100*soFar/total);
^
Cluster.c:794:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:978:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c] = (k - 1) & 0xFF; // length of run
^
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:1213:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = (unsigned char)lastHit;
^
Compression.c:542:36: note: 'lastHit' 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:629:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
int run, lastTriplet, lastCase;
^
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:1086:12: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
dict[word] = j;
^
Compression.c:542:17: note: 'dict' was declared here
unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -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: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: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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
-0.816507461,-2.5401714,-1.647430026,-1.184658548
^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
-0.141370102,-0.439805276,-0.285236035,-0.205111781
^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
0,0,0,0
^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Diff.c -o Diff.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:135:27: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
^
FindFrameshifts.c:135:24: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
^
FindFrameshifts.c:135:21: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c GetPools.c -o GetPools.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Import.c -o Import.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c InformationContent.c -o InformationContent.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9,-8.4,-7.8,-7.2
^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2,-22.4,-21.0,-20.4
^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
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]]);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:454:24: note: 'utilsPackage' was declared here
SEXP percentComplete, utilsPackage;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:454:7: note: 'percentComplete' was declared here
SEXP percentComplete, utilsPackage;
^
MultiMatch.c:543:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from NNLS.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Order.c -o Order.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:833:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]];// + 1;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:37:0,
from PredictDBN.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/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:445:10: note: 'MI2' was declared here
double *MI2, *rowMax, *colMax;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -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:233:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
states[j] = 'C';
^
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
double H, E, C, sum, *rans;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Translate.c -o Translate.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c VectorSums.c -o VectorSums.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/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 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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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
CorrectFrameshifts html
CreateChimeras html
DB2Seqs html
DECIPHER-package html
DesignArray html
DesignPrimers html
DesignProbes html
DesignSignatures html
DigestDNA html
Disambiguate html
DistanceMatrix html
FindChimeras html
FindSynteny html
FormGroups html
HEC_MI html
IdClusters html
IdConsensus html
IdLengths html
IdTaxa html
IdentifyByRank html
LearnTaxa html
MIQS html
MODELS html
MaskAlignment html
MeltDNA html
NNLS 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
deltaGrules html
deltaHrules html
deltaSrules 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
-11.5, -7.8, -7, -8.3,
^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
-36.4, -21.6, -19.7, -23.9,
^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9, -8.4, -7.8, -7.2,
^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2, -22.4, -21, -20.4,
^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
-6.6, -10.17, -7.65, -5.76,
^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
-18.38, -26.03, -19.18, -15.67,
^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:420:72: 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:420:67: 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -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]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:978:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c] = (k - 1) & 0xFF; // length of run
^
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:1213:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
p[c++] = (unsigned char)lastHit;
^
Compression.c:542:36: note: 'lastHit' 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:629:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
int run, lastTriplet, lastCase;
^
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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
-0.816507461,-2.5401714,-1.647430026,-1.184658548
^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
-0.141370102,-0.439805276,-0.285236035,-0.205111781
^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
0,0,0,0
^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Diff.c -o Diff.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:318:12: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (C[k*rc + j*r + i] >= 0) {
^
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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from FindFrameshifts.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c GetPools.c -o GetPools.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Import.c -o Import.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c InformationContent.c -o InformationContent.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
-7.9,-8.4,-7.8,-7.2
^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
-22.2,-22.4,-21.0,-20.4
^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
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]]);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:454:24: note: 'utilsPackage' was declared here
SEXP percentComplete, utilsPackage;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define eval Rf_eval
^
MultiMatch.c:454:7: note: 'percentComplete' was declared here
SEXP percentComplete, utilsPackage;
^
MultiMatch.c:543:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
before = *rPercentComplete;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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 C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:40:0,
from NNLS.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rinternals.h:1411:16: 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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Order.c -o Order.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:833:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
range2[0] = nucs[pos[prev]];// + 1;
^
In file included from C:/Users/BIOCBU~1/BBS-3~1.10-/R/include/Rdefines.h:37:0,
from PredictDBN.c:11:
C:/Users/BIOCBU~1/BBS-3~1.10-/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:445:10: note: 'MI2' was declared here
double *MI2, *rowMax, *colMax;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Translate.c -o Translate.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c VectorSums.c -o VectorSums.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/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 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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.14.0.zip
* DONE (DECIPHER)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DECIPHER' successfully unpacked and MD5 sums checked
