############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## % 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