############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'DECIPHER' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function 'alignProfiles._omp_fn.0': AlignProfiles.c:437:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 437 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:51: note: 'lGs' was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:435:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 435 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:46: note: 'lGp' was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0': AlignProfiles.c:1290:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized] 1290 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:51: note: 'lGs' was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1288:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized] 1288 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:819:46: note: 'lGp' was declared here 819 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function 'alignProfiles': AlignProfiles.c:388:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 388 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS) | ^~~ AlignProfiles.c:81:17: note: 'subM' was declared here 81 | double *subM; | ^~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o CalculateDeltaG.c: In function 'calculateHairpinDeltaG': CalculateDeltaG.c:463:36: warning: 's1' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:29: note: 's1' was declared here 375 | int i, j, k, count, s1, s2; | ^~ CalculateDeltaG.c:463:49: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:375:33: note: 's2' was declared here 375 | int i, j, k, count, s1, s2; | ^~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function 'calculateFISH': CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces] 25 | double dH_DR[4][4] = { | ^ 26 | -11.5, -7.8, -7, -8.3, | { } 27 | -10.4, -12.8, -16.3, -9.1, | { } 28 | -8.6, -8, -9.3, -5.9, | { } 29 | -7.8, -5.5, -9, -7.8 | { 30 | }; | } CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces] 31 | double dS_DR[4][4] = { | ^ 32 | -36.4, -21.6, -19.7, -23.9, | { } 33 | -28.4, -31.9, -47.1, -23.5, | { } 34 | -22.9, -17.1, -23.2, -12.3, | { } 35 | -23.2, -13.5, -26.1, -21.9 | { 36 | }; | } CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces] 37 | double dH_DD[4][4] = { | ^ 38 | -7.9, -8.4, -7.8, -7.2, | { } 39 | -8.5, -8, -10.6, -7.8, | { } 40 | -8.2, -9.8, -8, -8.4, | { } 41 | -7.2, -8.2, -8.5, -7.9 | { 42 | }; | } CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces] 43 | double dS_DD[4][4] = { | ^ 44 | -22.2, -22.4, -21, -20.4, | { } 45 | -22.7, -19.9, -27.2, -21, | { } 46 | -22.2, -24.4, -19.9, -22.4, | { } 47 | -21.3, -22.2, -22.7, -22.2 | { 48 | }; | } CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces] 49 | double dH_RR[4][4] = { | ^ 50 | -6.6, -10.17, -7.65, -5.76, | { } 51 | -10.56, -12.21, -7.95, -7.65, | { } 52 | -13.37, -14.21, -12.21, -10.17, | { } 53 | -8.11, -13.37, -10.56, -6.6 | { 54 | }; | } CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces] 55 | double dS_RR[4][4] = { | ^ 56 | -18.38, -26.03, -19.18, -15.67, | { } 57 | -28.25, -30.02, -19.18, -19.18, | { } 58 | -35.68, -34.85, -30.02, -26.03, | { } 59 | -22.59, -35.68, -28.25, -18.38 | { 60 | }; | } gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o ChainSegments.c: In function 'chainSegments': ChainSegments.c:524:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:490:93: note: 'upY' was declared here 490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ ChainSegments.c:524:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:490:88: note: 'upX' was declared here 490 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o Cluster.c: In function 'cluster._omp_fn.0': Cluster.c:418:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 418 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster._omp_fn.1': Cluster.c:442:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 442 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function 'cluster': Cluster.c:408:41: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized] 408 | #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads) | ^~~ Cluster.c:283:17: note: 'nDiv' was declared here 283 | double *nDiv; | ^~~~ Cluster.c:392:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized] 392 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:57: note: 'minC' was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o ClusterML.c: In function 'clusterML': ClusterML.c:1293:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1170:17: note: 'node' was declared here 1170 | double *node; | ^~~~ ClusterML.c:1293:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1206:14: note: 'Up' was declared here 1206 | int *Up; | ^~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function 'clusterMP._omp_fn.0': ClusterMP.c:165:41: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized] 165 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:153:30: note: 'P' was declared here 153 | int *P; | ^ ClusterMP.c:98:22: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized] 98 | int i, j, k, m, w; | ^ ClusterMP.c: In function 'clusterMP': ClusterMP.c:140:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:126:14: note: 'Up' was declared here 126 | int *Up; | ^~ ClusterMP.c:140:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:111:17: note: 'lengths' was declared here 111 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:140:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:112:14: note: 'nodes' was declared here 112 | int *nodes, *subM; | ^~~~~ ClusterMP.c:140:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:112:22: note: 'subM' was declared here 112 | int *nodes, *subM; | ^~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o Compression.c: In function 'nbit._omp_fn.0': Compression.c:1241:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized] 1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:631:26: note: 'lastTriplet' was declared here 631 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1011:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized] 1011 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:544:37: note: 'word' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1012:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized] 1012 | count++; | ~~~~~^~ Compression.c:544:43: note: 'count' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:545:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized] 545 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:1215:58: warning: 'lastHit' may be used uninitialized [-Wmaybe-uninitialized] 1215 | p[c++] = (unsigned char)lastHit; | ^~~~~~~~~~~~~~~~~~~~~~ Compression.c:544:50: note: 'lastHit' was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o In function 'runsAA', inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3: ConsensusSequence.c:454:50: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized] 454 | if (lastGap < (s - 2)) // ensure continuity before the run | ~~~^~~~ ConsensusSequence.c: In function 'consensusProfileAA': ConsensusSequence.c:397:30: note: 'lastPos' was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c: In function 'colScores': ConsensusSequence.c:2043:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2043 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:1930:37: note: 'curr' was declared here 1930 | double weight, total, prev, curr; | ^~~~ ConsensusSequence.c: In function 'colScoresAA': ConsensusSequence.c:2186:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized] 2186 | if (tGaps && curr > 0) { | ~~~~~~^~~~~~~~~~~ ConsensusSequence.c:2073:37: note: 'curr' was declared here 2073 | double weight, total, prev, curr; | ^~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function 'designProbes': DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces] 70 | double NN[4][4] = { | ^ 71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 75 | }; | } DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces] 77 | double PM[4][4] = { | ^ 78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 82 | }; | } DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces] 84 | double sMM[4][5][5][4] = { | ^ 85 | 0,0,0,0 | {{{ 86 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 87 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 88 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 89 | ,0.75,0.65,0.69,0.78 | }{ 90 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 91 | ,0,0,0,0 | }{ 92 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 93 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 94 | ,0.75,0.65,0.69,0.78 | }{ 95 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 96 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 97 | ,0,0,0,0 | }{ 98 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 99 | ,0.75,0.65,0.69,0.78 | }{ 100 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 101 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 102 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 103 | ,0,0,0,0 | }{ 104 | ,0.75,0.65,0.69,0.78 | }{ 105 | ,0.75,0.65,0.69,0.78 | - | }},{{ 106 | ,0.75,0.65,0.69,0.78 | }{ 107 | ,0.75,0.65,0.69,0.78 | }{ 108 | ,0.76,0.65,0.69,0.78 | }{ 109 | ,0,0,0,0 | }{ 110 | ,0,0,0,0 | - | }}},{{{ 111 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 112 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 113 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 114 | ,0.65,0.55,0.48,0.69 | }{ 115 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 116 | ,0,0,0,0 | }{ 117 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 118 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 119 | ,0.65,0.56,0.49,0.69 | }{ 120 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 121 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 122 | ,0,0,0,0 | }{ 123 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 124 | ,0.65,0.56,0.49,0.69 | }{ 125 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 126 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 127 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 128 | ,0,0,0,0 | }{ 129 | ,0.65,0.55,0.48,0.69 | }{ 130 | ,0.65,0.55,0.48,0.69 | - | }},{{ 131 | ,0.65,0.56,0.49,0.69 | }{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.55,0.48,0.69 | }{ 134 | ,0,0,0,0 | }{ 135 | ,0,0,0,0 | - | }}},{{{ 136 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 137 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 138 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 139 | ,0.68,0.46,0.55,0.65 | }{ 140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 141 | ,0,0,0,0 | }{ 142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 143 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 144 | ,0.68,0.47,0.56,0.65 | }{ 145 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 146 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 147 | ,0,0,0,0 | }{ 148 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 149 | ,0.68,0.47,0.56,0.65 | }{ 150 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 151 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 152 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 153 | ,0,0,0,0 | }{ 154 | ,0.68,0.46,0.55,0.65 | }{ 155 | ,0.68,0.46,0.55,0.65 | - | }},{{ 156 | ,0.68,0.47,0.56,0.65 | }{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.46,0.55,0.65 | }{ 159 | ,0,0,0,0 | }{ 160 | ,0,0,0,0 | - | }}},{{{ 161 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 162 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 163 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 164 | ,0.85,0.68,0.65,0.76 | }{ 165 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 166 | ,0,0,0,0 | }{ 167 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 168 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 169 | ,0.85,0.68,0.65,0.75 | }{ 170 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 171 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 172 | ,0,0,0,0 | }{ 173 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 174 | ,0.85,0.68,0.65,0.75 | }{ 175 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 176 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 177 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 178 | ,0,0,0,0 | }{ 179 | ,0.85,0.68,0.65,0.75 | }{ 180 | ,0.85,0.68,0.65,0.75 | - | }},{{ 181 | ,0.85,0.68,0.65,0.75 | }{ 182 | ,0.85,0.68,0.65,0.75 | }{ 183 | ,0.85,0.68,0.65,0.75 | }{ 184 | ,0,0,0,0 | }{ 185 | }; | }}} DesignProbes.c: In function 'designProbes._omp_fn.0': DesignProbes.c:837:60: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized] 837 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:269:58: note: 'lastCycle' was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:837:60: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized] 837 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:269:69: note: 'thisCycle' was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function 'firstSeqsPosEqual': DistanceMatrix.c:796:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 796 | if (!ci) | ^~ DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 799 | while (i < ex) { | ^~~~~ DistanceMatrix.c:818:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 818 | if (!cj) | ^~ DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 821 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function 'computeOverlap._omp_fn.0': DistanceMatrix.c:1374:66: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:92: note: 'OV' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ DistanceMatrix.c:1374:66: warning: 'off' may be used uninitialized [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:96: note: 'off' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~~ DistanceMatrix.c:1053:53: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized] 1053 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1028:29: note: 'one' was declared here 1028 | int one, two; | ^~~ DistanceMatrix.c:1390:52: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized] 1390 | if (o == 1) { | ^ DistanceMatrix.c:883:112: note: 'o' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^ DistanceMatrix.c:1393:91: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized] 1393 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:883:88: note: 'ov' was declared here 883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax; | ^~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function 'pop': EnumerateSequence.c:545:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 545 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function 'enumerateSequence': EnumerateSequence.c:358:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:317:14: note: 'mN' was declared here 317 | int *mN; | ^~ EnumerateSequence.c:358:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:13: note: 'tot' was declared here 318 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function 'enumerateSequenceReducedAA': EnumerateSequence.c:955:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:907:14: note: 'mN' was declared here 907 | int *mN; | ^~ EnumerateSequence.c:955:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:908:13: note: 'tot' was declared here 908 | int tot; // total number of k-mers | ^~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function 'findFrameshifts': FindFrameshifts.c:464:43: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 464 | *rPercentComplete = floor(100*(double)(s + 1)/f_length); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here 160 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from FindFrameshifts.c:11: C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 903 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:14: note: 'percentComplete' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 903 | #define eval Rf_eval FindFrameshifts.c:467:33: note: in expansion of macro 'eval' 467 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ FindFrameshifts.c:317:34: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:28: note: 'I' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:317:43: warning: 'J' may be used uninitialized [-Wmaybe-uninitialized] 317 | while (i > 0 && j > 0) { | ~~^~~ FindFrameshifts.c:135:31: note: 'J' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ FindFrameshifts.c:376:28: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized] 376 | if (k == 1) { | ^ FindFrameshifts.c:135:34: note: 'K' was declared here 135 | int s, o, i, j, k, I, J, K, n, m, w, r, c, rc; | ^ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function 'scoreCodonModel': GeneFinding.c:421:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 421 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:388:22: note: 'x_i.ptr' was declared here 388 | Chars_holder x_i; | ^~~ GeneFinding.c:431:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized] 431 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:371:32: note: 'lastVal' was declared here 371 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function 'startCodonModel': GeneFinding.c:795:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 795 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:771:22: note: 'x_i.ptr' was declared here 771 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStartCodonModel': GeneFinding.c:896:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 896 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:868:22: note: 'x_i.ptr' was declared here 868 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'initialCodonModel': GeneFinding.c:951:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 951 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:928:22: note: 'x_i.ptr' was declared here 928 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreInitialCodonModel': GeneFinding.c:1058:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1058 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1031:22: note: 'x_i.ptr' was declared here 1031 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'terminationCodonModel': GeneFinding.c:1115:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1115 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1092:22: note: 'x_i.ptr' was declared here 1092 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreTerminationCodonModel': GeneFinding.c:1215:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1215 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1188:22: note: 'x_i.ptr' was declared here 1188 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'getRegion': GeneFinding.c:1316:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1316 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1252:22: note: 'x_i.ptr' was declared here 1252 | Chars_holder x_i; | ^~~ GeneFinding.c:1313:51: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized] 1313 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1252:22: note: 'x_i.length' was declared here 1252 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'autocorrelationModel': GeneFinding.c:1378:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1378 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1350:22: note: 'x_i.ptr' was declared here 1350 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreAutocorrelationModel': GeneFinding.c:1495:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1495 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1461:22: note: 'x_i.ptr' was declared here 1461 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'couplingModel': GeneFinding.c:1597:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1597 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1573:22: note: 'x_i.ptr' was declared here 1573 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreCouplingModel': GeneFinding.c:1711:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1711 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1681:22: note: 'x_i.ptr' was declared here 1681 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'nucleotideBiasModel': GeneFinding.c:1826:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1826 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1788:22: note: 'x_i.ptr' was declared here 1788 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreNucleotideBiasModel': GeneFinding.c:1913:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1913 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1882:22: note: 'x_i.ptr' was declared here 1882 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'upstreamMotifModel': GeneFinding.c:1992:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 1992 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1950:22: note: 'x_i.ptr' was declared here 1950 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreUpstreamMotifModel': GeneFinding.c:2092:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2092 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2057:22: note: 'x_i.ptr' was declared here 2057 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreRunLengthModel': GeneFinding.c:2307:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2307 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2276:22: note: 'x_i.ptr' was declared here 2276 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'stopCodonModel': GeneFinding.c:2423:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2423 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2399:22: note: 'x_i.ptr' was declared here 2399 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'scoreStopCodonModel': GeneFinding.c:2524:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2524 | val = getBase(x_i.ptr[j--]); | ^ GeneFinding.c:2496:22: note: 'x_i.ptr' was declared here 2496 | Chars_holder x_i; | ^~~ GeneFinding.c: In function 'codonFrequencies': GeneFinding.c:2577:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized] 2577 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2554:22: note: 'x_i.ptr' was declared here 2554 | Chars_holder x_i; | ^~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function 'meltPolymer': MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces] 79 | double dH[4][4] = { | ^ 80 | -7.9,-8.4,-7.8,-7.2 | { 81 | ,-8.5,-8.0,-10.6,-7.8 | }{ 82 | ,-8.2,-9.8,-8.0,-8.4 | }{ 83 | ,-7.2,-8.2,-8.5,-7.9 | }{ 84 | }; | } MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces] 88 | double dS[4][4] = { | ^ 89 | -22.2,-22.4,-21.0,-20.4 | { 90 | ,-22.7,-19.9,-27.2,-21.0 | }{ 91 | ,-22.2,-24.4,-19.9,-22.4 | }{ 92 | ,-21.3,-22.2,-22.7,-22.2 | }{ 93 | }; | } MeltPolymer.c:406:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized] 406 | SET_VECTOR_ELT(ret, s, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ MeltPolymer.c:53:19: note: 'ans' was declared here 53 | SEXP ret, ans; | ^~~ MeltPolymer.c:358:41: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~~~~~~~~~~~~~~~~ MeltPolymer.c:54:17: note: 'rans' was declared here 54 | double *rans; | ^~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o NNLS.c: In function 'NNLS': NNLS.c:77:51: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 77 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:39:34: note: 'rPercentComplete' was declared here 39 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41, from NNLS.c:16: C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 903 | #define eval Rf_eval NNLS.c:81:41: note: in expansion of macro 'eval' 81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:47:14: note: 'percentComplete' was declared here 47 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:903:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 903 | #define eval Rf_eval NNLS.c:81:41: note: in expansion of macro 'eval' 81 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:47:31: note: 'utilsPackage' was declared here 47 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function 'alignPair._omp_fn.0': PairwiseAlignment.c:445:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized] 445 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:175:24: note: 'p3' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:446:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized] 446 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:175:29: note: 'p4' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:449:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized] 449 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:175:14: note: 'p1' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized] 450 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:175:19: note: 'p2' was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function 'alignPairs': PairwiseAlignment.c:1107:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1035:25: note: 'rPercentComplete' was declared here 1035 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1107:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1037:14: note: 'percentComplete' was declared here 1037 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1107:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1037:31: note: 'utilsPackage' was declared here 1037 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o PredictDBN.c: In function 'predictDBN': PredictDBN.c:597:25: warning: 'leftSymbol' may be used uninitialized [-Wmaybe-uninitialized] 597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:485:14: note: 'leftSymbol' was declared here 485 | char leftSymbol, rightSymbol; | ^~~~~~~~~~ PredictDBN.c:597:25: warning: 'rightSymbol' may be used uninitialized [-Wmaybe-uninitialized] 597 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:485:26: note: 'rightSymbol' was declared here 485 | char leftSymbol, rightSymbol; | ^~~~~~~~~~~ In file included from C:/Users/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:38, from PredictDBN.c:16: C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/RS.h:55:25: warning: 'MI' may be used uninitialized [-Wmaybe-uninitialized] 55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:1071:9: note: in expansion of macro 'Free' 1071 | Free(MI); | ^~~~ PredictDBN.c:236:17: note: 'MI' was declared here 236 | double *MI = Calloc(tot*tot, double); // initialized to zero | ^~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictHEC.c -o PredictHEC.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Search.c -o Search.o Search.c: In function 'searchIndex._omp_fn.0': Search.c:475:75: warning: 'maxLen' may be used uninitialized [-Wmaybe-uninitialized] 475 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:449:37: note: 'maxLen' was declared here 449 | int maxLen; // maximum observed length | ^~~~~~ Search.c:443:51: warning: 's_j.ptr' may be used uninitialized [-Wmaybe-uninitialized] 443 | Chars_holder p_i, s_j; | ^~~ Search.c: In function 'searchIndex': Search.c:208:17: warning: 'sM' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:104:17: note: 'sM' was declared here 104 | double *sM, dS; | ^~ Search.c:208:17: warning: 'dS' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:104:21: note: 'dS' was declared here 104 | double *sM, dS; | ^~ Search.c:208:17: warning: 'lkup_row' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:105:14: note: 'lkup_row' was declared here 105 | int *lkup_row, *lkup_col; | ^~~~~~~~ Search.c:208:17: warning: 'lkup_col' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:105:25: note: 'lkup_col' was declared here 105 | int *lkup_row, *lkup_col; | ^~~~~~~~ Search.c:208:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:133:25: note: 'rPercentComplete' was declared here 133 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:208:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:135:14: note: 'percentComplete' was declared here 135 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:208:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:135:31: note: 'utilsPackage' was declared here 135 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:208:17: warning: 'matrices' may be used uninitialized [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:201:16: note: 'matrices' was declared here 201 | int ***matrices; | ^~~~~~~~ Search.c:943:38: warning: 'anchors' may be used uninitialized [-Wmaybe-uninitialized] 943 | int *anchor = anchors[j]; | ^~~~~~ Search.c:888:15: note: 'anchors' was declared here 888 | int **anchors; // pointers to anchor positions | ^~~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.c -o Utils.o Utils.c: In function 'splitPartitions': Utils.c:982:35: warning: 'change' may be used uninitialized [-Wmaybe-uninitialized] 982 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:976:13: note: 'change' was declared here 976 | int change; // index before start of partition | ^~~~~~ gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o 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 ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DECIPHER)