############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘DECIPHER’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’: AlignProfiles.c:438:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 438 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:51: note: ‘lGs’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:436:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 436 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:62:46: note: ‘lGp’ was declared here 62 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’: AlignProfiles.c:1291:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized] 1291 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:51: note: ‘lGs’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1289:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:820:46: note: ‘lGp’ was declared here 820 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:389:25: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 389 | #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:82:17: note: ‘subM’ was declared here 82 | double *subM; | ^~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o CalculateFISH.c: In function ‘calculateFISH’: CalculateFISH.c:25:30: 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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o ChainSegments.c: In function ‘chainSegments’: ChainSegments.c:525:49: warning: ‘upY’ may be used uninitialized [-Wmaybe-uninitialized] 525 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:491:93: note: ‘upY’ was declared here 491 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ ChainSegments.c:525:49: warning: ‘upX’ may be used uninitialized [-Wmaybe-uninitialized] 525 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:491:88: note: ‘upX’ was declared here 491 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY; | ^~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Cluster.c -o Cluster.o Cluster.c: In function ‘cluster._omp_fn.0’: Cluster.c:439:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 439 | 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._omp_fn.1’: Cluster.c:469:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 469 | 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.2’: Cluster.c:493:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 493 | 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:848:44: warning: ‘minCols’ may be used uninitialized [-Wmaybe-uninitialized] 848 | if (minCols[rowIndices[i]] == (minRow + 1)) { | ^ Cluster.c:277:14: note: ‘minCols’ was declared here 277 | int *minCols; | ^~~~~~~ Cluster.c:459:41: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized] 459 | #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:413:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized] 413 | 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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterME.c -o ClusterME.o ClusterME.c: In function ‘clusterME’: ClusterME.c:322:101: warning: ‘LLRL’ may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:24: note: ‘LLRL’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:322:101: warning: ‘LRRL’ may be used uninitialized [-Wmaybe-uninitialized] 322 | subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac | ~~~~~^~~~~~ ClusterME.c:284:30: note: ‘LRRL’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: ‘LLRR’ may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:36: note: ‘LLRR’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ ClusterME.c:323:101: warning: ‘LRRR’ may be used uninitialized [-Wmaybe-uninitialized] 323 | subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc | ~~~~~^~~~~~ ClusterME.c:284:42: note: ‘LRRR’ was declared here 284 | double LLRL, LRRL, LLRR, LRRR; | ^~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterML.c -o ClusterML.o ClusterML.c: In function ‘clusterML’: ClusterML.c:1743:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized] 1743 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1610:17: note: ‘node’ was declared here 1610 | double *node; | ^~~~ ClusterML.c:1743:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 1743 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ ClusterML.c:1656:14: note: ‘Up’ was declared here 1656 | int *Up; | ^~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o ClusterMP.c: In function ‘clusterMP._omp_fn.0’: ClusterMP.c:190:71: warning: ‘temp_nodes’ may be used uninitialized [-Wmaybe-uninitialized] 190 | temp_nodes[j] = 0; | ~~~~~~~~~~~~~~^~~ ClusterMP.c:163:34: note: ‘temp_nodes’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~~ ClusterMP.c:465:49: warning: ‘temp_lengths’ may be used uninitialized [-Wmaybe-uninitialized] 465 | *(temp_lengths + j) += *(S + w*c + m)*weight; | ^~~~~~~~~~~~~~~~~~~ ClusterMP.c:162:38: note: ‘temp_lengths’ was declared here 162 | double *temp_score, *temp_lengths; | ^~~~~~~~~~~~ ClusterMP.c:485:73: warning: ‘temp_subM’ may be used uninitialized [-Wmaybe-uninitialized] 485 | *(temp_subM + c*m + w - 1) += weight; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:163:22: note: ‘temp_subM’ was declared here 163 | int *temp_subM, *temp_nodes; | ^~~~~~~~~ ClusterMP.c:202:49: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized] 202 | allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClusterMP.c:185:38: note: ‘P’ was declared here 185 | int *P; | ^ ClusterMP.c:385:61: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 385 | *(R + 3*c*n + m) = 0; | ^ ClusterMP.c:105:22: note: ‘m’ was declared here 105 | int i, j, k, m, w; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:159:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:128:17: note: ‘lengths’ was declared here 128 | double *lengths, *score; | ^~~~~~~ ClusterMP.c:159:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:20: note: ‘nodes’ was declared here 129 | int size, *nodes, *subM; | ^~~~~ ClusterMP.c:159:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:129:28: note: ‘subM’ was declared here 129 | int size, *nodes, *subM; | ^~~~ ClusterMP.c:159:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 159 | #pragma omp parallel num_threads(nthreads) | ^~~ ClusterMP.c:145:14: note: ‘Up’ was declared here 145 | int *Up; | ^~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o Compression.c: In function ‘nbit._omp_fn.0’: Compression.c:1328:25: warning: ‘dict’ may be used uninitialized [-Wmaybe-uninitialized] 1328 | free(dict); | ^~~~~~~~~~ Compression.c:545:31: note: ‘dict’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1242:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized] 1242 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:632:26: note: ‘lastTriplet’ was declared here 632 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1012:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized] 1012 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:545:37: note: ‘word’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1013:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 1013 | count++; | ~~~~~^~ Compression.c:545:43: note: ‘count’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:546:41: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized] 546 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:1216:58: warning: ‘lastHit’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | p[c++] = (unsigned char)lastHit; | ^~~~~~~~~~~~~~~~~~~~~~ Compression.c:545:50: note: ‘lastHit’ was declared here 545 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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:1940:17: warning: ‘DBN’ may be used uninitialized [-Wmaybe-uninitialized] 1940 | double *DBN, *s; | ^~~ ConsensusSequence.c:1941:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized] 1941 | int do_DBN, n, l, d; | ^ 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:2083:17: warning: ‘HEC’ may be used uninitialized [-Wmaybe-uninitialized] 2083 | double *HEC, *s; | ^~~ ConsensusSequence.c:2084:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized] 2084 | int do_HEC, n, l, d; | ^ 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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o DesignProbes.c: In function ‘designProbes’: DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces] 71 | double NN[4][4] = { | ^ 72 | -0.816507461,-2.5401714,-1.647430026,-1.184658548 | { 73 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026 | }{ 74 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714 | }{ 75 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461 | }{ 76 | }; | } DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces] 78 | double PM[4][4] = { | ^ 79 | -0.141370102,-0.439805276,-0.285236035,-0.205111781 | { 80 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035 | }{ 81 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276 | }{ 82 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102 | }{ 83 | }; | } DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces] 85 | double sMM[4][5][5][4] = { | ^ 86 | 0,0,0,0 | {{{ 87 | ,1.545032445,1.254355018,1.491691514,1.329138183 | }{ 88 | ,1.150635633,0.582415494,1.075877275,1.187937642 | }{ 89 | ,1.203555051,1.001540513,0.864287715,0.717125848 | }{ 90 | ,0.75,0.65,0.69,0.78 | }{ 91 | ,0.630005348,0.18553379,0.730763505,0.709272397 | - | }},{{ 92 | ,0,0,0,0 | }{ 93 | ,0.856582783,-0.143236405,0.716721488,0.603652831 | }{ 94 | ,0.851622883,0.653168672,0.676545316,1.187937642 | }{ 95 | ,0.75,0.65,0.69,0.78 | }{ 96 | ,1.231861002,0.746214538,1.087821916,0.989140748 | - | }},{{ 97 | ,1.822113278,1.270687029,1.336192565,1.364584949 | }{ 98 | ,0,0,0,0 | }{ 99 | ,1.443665704,1.385046493,1.256013166,1.329138183 | }{ 100 | ,0.75,0.65,0.69,0.78 | }{ 101 | ,1.478009492,0.882097231,1.20450984,1.061002478 | - | }},{{ 102 | ,1.496720812,0.846496194,0.967868114,0.989140748 | }{ 103 | ,0.766581547,-0.024857805,0.50754303,0.709272397 | }{ 104 | ,0,0,0,0 | }{ 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 | ,0.75,0.65,0.69,0.78 | }{ 109 | ,0.76,0.65,0.69,0.78 | }{ 110 | ,0,0,0,0 | }{ 111 | ,0,0,0,0 | - | }}},{{{ 112 | ,1.295827995,0.84547091,0.91019099,1.256013166 | }{ 113 | ,0.755889609,0.241428373,0.396379912,0.676545316 | }{ 114 | ,0.99945386,0.740323132,0.435659206,0.864287715 | }{ 115 | ,0.65,0.55,0.48,0.69 | }{ 116 | ,0.843147406,0.101248351,0.49063599,0.50754303 | - | }},{{ 117 | ,0,0,0,0 | }{ 118 | ,1.0651638,0.249934344,0.699352949,0.716721488 | }{ 119 | ,0.871921533,0.59458138,0.396379912,1.075877275 | }{ 120 | ,0.65,0.56,0.49,0.69 | }{ 121 | ,1.07531714,0.318907854,0.653287717,0.967868114 | - | }},{{ 122 | ,1.099899195,0.730184613,0.661798984,1.336192565 | }{ 123 | ,0,0,0,0 | }{ 124 | ,1.45897431,1.318532145,0.91019099,1.491691514 | }{ 125 | ,0.65,0.56,0.49,0.69 | }{ 126 | ,1.242135174,0.894838095,1.108555445,1.20450984 | - | }},{{ 127 | ,0.911428974,0.524430101,0.653287717,1.087821916 | }{ 128 | ,0.503209827,0.274849491,0.49063599,0.730763505 | }{ 129 | ,0,0,0,0 | }{ 130 | ,0.65,0.55,0.48,0.69 | }{ 131 | ,0.65,0.55,0.48,0.69 | - | }},{{ 132 | ,0.65,0.56,0.49,0.69 | }{ 133 | ,0.65,0.56,0.49,0.69 | }{ 134 | ,0.65,0.55,0.48,0.69 | }{ 135 | ,0,0,0,0 | }{ 136 | ,0,0,0,0 | - | }}},{{{ 137 | ,1.100661785,0.969784756,1.318532145,1.385046493 | }{ 138 | ,0.565895968,-0.060347902,0.59458138,0.653168672 | }{ 139 | ,0.782168488,0.788161238,0.740323132,1.001540513 | }{ 140 | ,0.68,0.46,0.55,0.65 | }{ 141 | ,0.468913405,-0.469855984,0.274849491,-0.024857805 | - | }},{{ 142 | ,0,0,0,0 | }{ 143 | ,0.258195131,-0.70438632,0.249934344,-0.143236405 | }{ 144 | ,0.502914193,-0.060347902,0.241428373,0.582415494 | }{ 145 | ,0.68,0.47,0.56,0.65 | }{ 146 | ,0.584083861,0.258975454,0.524430101,0.846496194 | - | }},{{ 147 | ,0.968040559,0.797499702,0.730184613,1.270687029 | }{ 148 | ,0,0,0,0 | }{ 149 | ,1.081040749,0.969784756,0.84547091,1.254355018 | }{ 150 | ,0.68,0.47,0.56,0.65 | }{ 151 | ,1.048553951,0.728354541,0.894838095,0.882097231 | - | }},{{ 152 | ,0.88611252,0.258975454,0.318907854,0.746214538 | }{ 153 | ,0.239520858,-0.469855984,0.101248351,0.18553379 | }{ 154 | ,0,0,0,0 | }{ 155 | ,0.68,0.46,0.55,0.65 | }{ 156 | ,0.68,0.46,0.55,0.65 | - | }},{{ 157 | ,0.68,0.47,0.56,0.65 | }{ 158 | ,0.68,0.47,0.56,0.65 | }{ 159 | ,0.68,0.46,0.55,0.65 | }{ 160 | ,0,0,0,0 | }{ 161 | ,0,0,0,0 | - | }}},{{{ 162 | ,1.566899704,1.081040749,1.45897431,1.443665704 | }{ 163 | ,0.976725675,0.502914193,0.871921533,0.851622883 | }{ 164 | ,1.482046826,0.782168488,0.99945386,1.203555051 | }{ 165 | ,0.85,0.68,0.65,0.76 | }{ 166 | ,0.798628781,0.239520858,0.503209827,0.766581547 | - | }},{{ 167 | ,0,0,0,0 | }{ 168 | ,1.141098246,0.258195131,1.0651638,0.856582783 | }{ 169 | ,0.976725675,0.565895968,0.755889609,1.150635633 | }{ 170 | ,0.85,0.68,0.65,0.75 | }{ 171 | ,1.125403302,0.88611252,0.911428974,1.496720812 | - | }},{{ 172 | ,1.68169282,0.968040559,1.099899195,1.822113278 | }{ 173 | ,0,0,0,0 | }{ 174 | ,1.566899704,1.100661785,1.295827995,1.545032445 | }{ 175 | ,0.85,0.68,0.65,0.75 | }{ 176 | ,1.35948517,1.048553951,1.242135174,1.478009492 | - | }},{{ 177 | ,1.125403302,0.584083861,1.07531714,1.231861002 | }{ 178 | ,0.798628781,0.468913405,0.843147406,0.630005348 | }{ 179 | ,0,0,0,0 | }{ 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 | ,0.85,0.68,0.65,0.75 | }{ 185 | ,0,0,0,0 | }{ 186 | }; | }}} DesignProbes.c: In function ‘designProbes._omp_fn.0’: DesignProbes.c:838:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:58: note: ‘lastCycle’ was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:838:60: warning: ‘thisCycle’ may be used uninitialized [-Wmaybe-uninitialized] 838 | if (thisCycle < lastCycle) { | ^ DesignProbes.c:270:69: note: ‘thisCycle’ was declared here 270 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o DistanceMatrix.c: In function ‘firstSeqsPosEqual’: DistanceMatrix.c:805:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 805 | if (!ci) | ^~ DistanceMatrix.c:808:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 808 | while (i < ex) { | ^~~~~ DistanceMatrix.c:827:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 827 | if (!cj) | ^~ DistanceMatrix.c:830:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 830 | while (j < ey) { | ^~~~~ DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’: DistanceMatrix.c:1383:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized] 1383 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:892:92: note: ‘OV’ was declared here 892 | 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:1383:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized] 1383 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:892:96: note: ‘off’ was declared here 892 | 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:1062:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized] 1062 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1037:29: note: ‘one’ was declared here 1037 | int one, two; | ^~~ DistanceMatrix.c:1399:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized] 1399 | if (o == 1) { | ^ DistanceMatrix.c:892:112: note: ‘o’ was declared here 892 | 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:1402:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized] 1402 | sim[i] = (double)pos/((double)(ov + count + g2)); | ~~~^~~~~~~ DistanceMatrix.c:892:88: note: ‘ov’ was declared here 892 | 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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o EnumerateSequence.c: In function ‘pop’: EnumerateSequence.c:546:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 546 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function ‘enumerateSequence’: EnumerateSequence.c:359:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:318:14: note: ‘mN’ was declared here 318 | int *mN; | ^~ EnumerateSequence.c:359:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 359 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:319:13: note: ‘tot’ was declared here 319 | int tot; // total number of k-mers | ^~~ EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’: EnumerateSequence.c:956:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized] 956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:908:14: note: ‘mN’ was declared here 908 | int *mN; | ^~ EnumerateSequence.c:956:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized] 956 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:909:13: note: ‘tot’ was declared here 909 | int tot; // total number of k-mers | ^~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o FindFrameshifts.c: In function ‘findFrameshifts’: FindFrameshifts.c: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 /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 927 | #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; | ^~~~~~~~~~~~~~~ /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 927 | #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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o GeneFinding.c: In function ‘scoreCodonModel’: GeneFinding.c:422:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 422 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:389:22: note: ‘x_i.ptr’ was declared here 389 | Chars_holder x_i; | ^~~ GeneFinding.c:432:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized] 432 | if (val < 64 && lastVal < 64) | ~~~~~~~~^~~~ GeneFinding.c:372:32: note: ‘lastVal’ was declared here 372 | int i, j, s, fin, val, lastVal, dicodon; | ^~~~~~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:798:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 798 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:772:22: note: ‘x_i.ptr’ was declared here 772 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStartCodonModel’: GeneFinding.c:899:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 899 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:869:22: note: ‘x_i.ptr’ was declared here 869 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘initialCodonModel’: GeneFinding.c:952:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 952 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:929:22: note: ‘x_i.ptr’ was declared here 929 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreInitialCodonModel’: GeneFinding.c:1059:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1059 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1032:22: note: ‘x_i.ptr’ was declared here 1032 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘terminationCodonModel’: GeneFinding.c:1116:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1116 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1093:22: note: ‘x_i.ptr’ was declared here 1093 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreTerminationCodonModel’: GeneFinding.c:1216:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1189:22: note: ‘x_i.ptr’ was declared here 1189 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘getRegion’: GeneFinding.c:1317:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1317 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c:1253:22: note: ‘x_i.ptr’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c:1314:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized] 1314 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1253:22: note: ‘x_i.length’ was declared here 1253 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘autocorrelationModel’: GeneFinding.c:1379:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1351:22: note: ‘x_i.ptr’ was declared here 1351 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreAutocorrelationModel’: GeneFinding.c:1496:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1496 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1462:22: note: ‘x_i.ptr’ was declared here 1462 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘couplingModel’: GeneFinding.c:1598:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1598 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1574:22: note: ‘x_i.ptr’ was declared here 1574 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreCouplingModel’: GeneFinding.c:1712:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1712 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1682:22: note: ‘x_i.ptr’ was declared here 1682 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘nucleotideBiasModel’: GeneFinding.c:1827:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1827 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1789:22: note: ‘x_i.ptr’ was declared here 1789 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreNucleotideBiasModel’: GeneFinding.c:1914:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1914 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:1883:22: note: ‘x_i.ptr’ was declared here 1883 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘upstreamMotifModel’: GeneFinding.c:1993:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1993 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:1951:22: note: ‘x_i.ptr’ was declared here 1951 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreUpstreamMotifModel’: GeneFinding.c:2093:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2093 | val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]); | ^ GeneFinding.c:2058:22: note: ‘x_i.ptr’ was declared here 2058 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreRunLengthModel’: GeneFinding.c:2308:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2308 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2277:22: note: ‘x_i.ptr’ was declared here 2277 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘stopCodonModel’: GeneFinding.c:2426:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2426 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2400:22: note: ‘x_i.ptr’ was declared here 2400 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘scoreStopCodonModel’: GeneFinding.c:2527:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2527 | val += 16*getBase(x_i.ptr[j]); | ^ GeneFinding.c:2497:22: note: ‘x_i.ptr’ was declared here 2497 | Chars_holder x_i; | ^~~ GeneFinding.c: In function ‘codonFrequencies’: GeneFinding.c:2578:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 2578 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:2555:22: note: ‘x_i.ptr’ was declared here 2555 | Chars_holder x_i; | ^~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GetPools.c -o GetPools.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InformationContent.c -o InformationContent.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o MeltPolymer.c: In function ‘meltPolymer’: MeltPolymer.c:79:27: 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"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o NNLS.c: In function ‘NNLS’: NNLS.c:78:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 78 | *rPercentComplete = floor(100*((double)i + 1)/(double)l); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NNLS.c:40:34: note: ‘rPercentComplete’ was declared here 40 | int i, j, k, before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ In file included from /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rdefines.h:41, from NNLS.c:17: /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:14: note: ‘percentComplete’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ /home/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 927 | #define eval Rf_eval NNLS.c:82:41: note: in expansion of macro ‘eval’ 82 | eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage); | ^~~~ NNLS.c:48:31: note: ‘utilsPackage’ was declared here 48 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o Order.c: In function ‘radixOrder’: Order.c:169:41: warning: ‘bounds’ may be used uninitialized [-Wmaybe-uninitialized] 169 | #pragma omp parallel num_threads(NTHREADS) | ^~~ Order.c:99:19: note: ‘bounds’ was declared here 99 | R_xlen_t *bounds; | ^~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’: PairwiseAlignment.c:446:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized] 446 | p3[0] = l1; | ~~~~~~^~~~ PairwiseAlignment.c:176:24: note: ‘p3’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:447:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized] 447 | p4[0] = l2 - j1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:29: note: ‘p4’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:450:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized] 450 | p1[0] = l2; | ~~~~~~^~~~ PairwiseAlignment.c:176:14: note: ‘p1’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:451:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized] 451 | p2[0] = l1 - i1; | ~~~~~~^~~~~~~~~ PairwiseAlignment.c:176:19: note: ‘p2’ was declared here 176 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function ‘alignPairs’: PairwiseAlignment.c:1108:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1036:25: note: ‘rPercentComplete’ was declared here 1036 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ PairwiseAlignment.c:1108:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1038:14: note: ‘percentComplete’ was declared here 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ PairwiseAlignment.c:1108:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 1108 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1038:31: note: ‘utilsPackage’ was declared here 1038 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o PredictDBN.c: In function ‘predictDBN’: PredictDBN.c:598:25: warning: ‘leftSymbol’ may be used uninitialized [-Wmaybe-uninitialized] 598 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:486:14: note: ‘leftSymbol’ was declared here 486 | char leftSymbol, rightSymbol; | ^~~~~~~~~~ PredictDBN.c:598:25: warning: ‘rightSymbol’ may be used uninitialized [-Wmaybe-uninitialized] 598 | Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictDBN.c:486:26: note: ‘rightSymbol’ was declared here 486 | char leftSymbol, rightSymbol; | ^~~~~~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o PredictHEC.c: In function ‘predictHEC’: PredictHEC.c:51:31: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized] 51 | double HEC[N], temp, *rans; | ^~~~ PredictHEC.c:247:43: warning: ‘states’ may be used uninitialized [-Wmaybe-uninitialized] 247 | states[j] = nms[0]; | ~~~~~~~~~~^~~~~~~~ PredictHEC.c:52:15: note: ‘states’ was declared here 52 | char *states; | ^~~~~~ PredictHEC.c:273:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 273 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:59:19: note: ‘ans’ was declared here 59 | SEXP ret, ans; | ^~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Search.c -o Search.o Search.c: In function ‘searchIndex._omp_fn.0’: Search.c:578:92: warning: ‘subScores’ may be used uninitialized [-Wmaybe-uninitialized] 578 | if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != NA_REAL) | ^ Search.c:317:33: note: ‘subScores’ was declared here 317 | double *subScores; // substitution scores (if maxIt > 0) | ^~~~~~~~~ Search.c:449:66: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 449 | score2[j] = score[o1[j]]; | ^ Search.c:282:33: note: ‘score’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~ Search.c:450:72: warning: ‘addScore’ may be used uninitialized [-Wmaybe-uninitialized] 450 | addScore2[j] = addScore[o1[j]]; | ^ Search.c:282:41: note: ‘addScore’ was declared here 282 | double *score, *addScore, *score2, *addScore2; | ^~~~~~~~ Search.c:587:83: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (deltaTarget >= maxSep + maxLen) { | ~~~~~~~^~~~~~~~ Search.c:560:45: note: ‘maxLen’ was declared here 560 | int maxLen; // maximum observed length | ^~~~~~ Search.c:555:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 555 | Chars_holder p_i, s_j; | ^~~ Search.c:626:55: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized] 626 | bound = s_j.length - 1; // right bound | ~~~~~~^~~~~~~~~~~~~~~~ Search.c:555:59: note: ‘s_j.length’ was declared here 555 | Chars_holder p_i, s_j; | ^~~ Search.c:882:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized] 882 | Chars_holder p_i, s_j; | ^~~ Search.c:1150:72: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized] 1150 | anchor[k++] = posQuery[p] + len[p] - 1; | ^ Search.c:370:30: note: ‘len’ was declared here 370 | int *len; // length of each hit | ^~~ Search.c:1139:58: warning: ‘chain’ may be used uninitialized [-Wmaybe-uninitialized] 1139 | while (p != chain[p]) { | ^ Search.c:369:30: note: ‘chain’ was declared here 369 | int *chain; // set of joined hits per match | ^~~~~ Search.c:371:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 371 | int *res; // indices of results | ^~~ Search.c: In function ‘searchIndex’: Search.c:224:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:17: note: ‘sM’ was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:111:21: note: ‘dS’ was declared here 111 | double *sM, dS; | ^~ Search.c:224:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:14: note: ‘lkup_row’ was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:224:17: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:25: note: ‘lkup_col’ was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~~~~~~ Search.c:224:17: warning: ‘pwv’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:112:36: note: ‘pwv’ was declared here 112 | int *lkup_row, *lkup_col, *pwv; | ^~~ Search.c:224:17: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:17: note: ‘scores’ was declared here 113 | double *scores, *addScores; | ^~~~~~ Search.c:224:17: warning: ‘addScores’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:113:26: note: ‘addScores’ was declared here 113 | double *scores, *addScores; | ^~~~~~~~~ Search.c:224:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:174:25: note: ‘rPercentComplete’ was declared here 174 | int before, v, *rPercentComplete; | ^~~~~~~~~~~~~~~~ Search.c:224:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:176:14: note: ‘percentComplete’ was declared here 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Search.c:224:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:176:31: note: ‘utilsPackage’ was declared here 176 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ Search.c:224:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized] 224 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:217:16: note: ‘matrices’ was declared here 217 | int ***matrices; | ^~~~~~~~ Search.c:1287:38: warning: ‘anchors’ may be used uninitialized [-Wmaybe-uninitialized] 1287 | int *anchor = anchors[j]; | ^~~~~~ Search.c:1232:15: note: ‘anchors’ was declared here 1232 | int **anchors; // pointers to anchor positions | ^~~~~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Utils.c -o Utils.o Utils.c: In function ‘splitPartitions’: Utils.c:990:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized] 990 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ Utils.c:984:13: note: ‘change’ was declared here 984 | int change; // index before start of partition | ^~~~~~ Utils.c: In function ‘matchColumns’: Utils.c:1198:55: warning: ‘lkup’ may be used uninitialized [-Wmaybe-uninitialized] 1198 | int val = lkup[(unsigned char)x_i.ptr[o[j]]]; | ^ Utils.c:1130:14: note: ‘lkup’ was declared here 1130 | int *lkup; | ^~~~ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c VectorSums.c -o VectorSums.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -shared -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.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 installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DECIPHER)