############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL DECIPHER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘DECIPHER’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:426:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 426 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:39: note: ‘lGp’ was declared here 61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0; | ^~~ AlignProfiles.c:428:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 428 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:61:44: note: ‘lGs’ 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:1270:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1270 | lGp *= tot; | ~~~~^~~~~~ AlignProfiles.c:810:39: note: ‘lGp’ was declared here 810 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c:1272:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1272 | lGs *= tot; | ~~~~^~~~~~ AlignProfiles.c:810:44: note: ‘lGs’ was declared here 810 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0; | ^~~ AlignProfiles.c: In function ‘alignProfiles’: AlignProfiles.c:379:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 379 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads) | ^~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:463:28: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ CalculateDeltaG.c:463:15: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) { | ~~~~^~~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:25:23: 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:31:23: 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:37:23: 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:43:23: 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:49:23: 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:55:23: 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/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:524:28: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized] 524 | if (minX == minY && upX == upY) { | ~~~~^~~~~~ ChainSegments.c:524:28: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:418:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 418 | minCs[i] = minC; | ~~~~~~~~~^~~~~~ Cluster.c:246:50: 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:442:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 442 | minCols[rowIndices[i]] = minC; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ Cluster.c:246:50: note: ‘minC’ was declared here 246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met; | ^~~~ Cluster.c: In function ‘cluster’: Cluster.c:464:52: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 464 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged | ^ Cluster.c:781:13: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized] 781 | nDiv[j] -= dMatrix2[length*colIndices[j] - colIndices[j]*(colIndices[j] + 1)/2 + rowIndices[i] - colIndices[j]]; // col sums | ^~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ClusterML.c -o ClusterML.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:38, from ClusterML.c:16: ClusterML.c: In function ‘clusterML’: /home/biocbuild/R/R-beta-2024-04-15_r86425/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized] 55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^~~~~~~~~~ ClusterML.c:1206:7: note: ‘Up’ was declared here 1206 | int *Up; | ^~ ClusterML.c:1293:10: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1293 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads) | ^~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:98:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized] 98 | int i, j, k, m, w; | ^ ClusterMP.c:153:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized] 153 | int *P; | ^ ClusterMP.c: In function ‘clusterMP’: ClusterMP.c:640:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized] 640 | free(Up); | ^~~~~~~~ ClusterMP.c:140:10: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized] 140 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads) | ^~~ ClusterMP.c:140:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized] ClusterMP.c:140:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Compositions.c -o Compositions.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:978:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 978 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run | ~~~^~~~ Compression.c:516:12: note: ‘k’ was declared here 516 | int i, j, k, pos; | ^ Compression.c:1012:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1012 | count++; | ~~~~~^~ Compression.c:544:29: note: ‘count’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~~ Compression.c:1011:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1011 | word = (word << 8) | (unsigned int)reorder(byte); | ~~~~~~^~~~~ Compression.c:544:23: note: ‘word’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ Compression.c:1214:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1214 | p[c++] = rev == 0 ? 254 : 255; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ Compression.c:545:27: note: ‘rev’ was declared here 545 | int lastTemp, currTemp, rev, len, len2, thresh = 1; | ^~~ Compression.c:558:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized] 558 | int lower = 0; | ^~~~~ Compression.c:1241:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) { | ~~~^~~~~~~~~~~~~~ Compression.c:631:12: note: ‘lastTriplet’ was declared here 631 | int run, lastTriplet, lastCase; | ^~~~~~~~~~~ Compression.c:1031:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1031 | lastHit = dict[(word >> k) & 0xFF]; | ^ Compression.c:544:17: note: ‘dict’ was declared here 544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0; | ^~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o ConsensusSequence.c: In function ‘consensusProfile’: ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1578 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘consensusProfileAA’: ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 455 | *(runs + s) += weight; | ^~ ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here 397 | int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1; | ^~~~~~~ ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1771 | double *HEC, *s; | ^~~ ConsensusSequence.c: In function ‘colScores’: ConsensusSequence.c:2046:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2046 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2046:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:1941:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1941 | int do_DBN, n, l, d; | ^ ConsensusSequence.c:1940:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1940 | double *DBN, *s; | ^~~ ConsensusSequence.c: In function ‘colScoresAA’: ConsensusSequence.c:2189:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2189 | *(rans + k) += GO*(curr*total); | ~~~~~^~~~~~~ ConsensusSequence.c:2189:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized] ConsensusSequence.c:2084:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2084 | int do_HEC, n, l, d; | ^ ConsensusSequence.c:2083:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2083 | double *HEC, *s; | ^~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:70:20: 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:77:20: 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:84:27: 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:838:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 838 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:269:37: note: ‘lastCycle’ was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ DesignProbes.c:838:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 838 | cycles += lastCycle - thisCycle; | ~~~~~~~~~~^~~~~~~~~~~ DesignProbes.c:269:48: note: ‘thisCycle’ was declared here 269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles; | ^~~~~~~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Diff.c -o Diff.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:796:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 796 | if (!ci) | ^~ DistanceMatrix.c:799:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 799 | while (i < ex) { | ^~~~~ DistanceMatrix.c:818:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 818 | if (!cj) | ^~ DistanceMatrix.c:821:4: 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:1053:11: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1053 | two != one) { | ~~~~^~~~~~ DistanceMatrix.c:1028:8: note: ‘one’ was declared here 1028 | int one, two; | ^~~ DistanceMatrix.c:1340:19: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1340 | if (w1 - p1 + p2 > w2 - t2) { | ~~~~~~~~^~~~ DistanceMatrix.c:883:69: note: ‘p2’ 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:1340:14: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1340 | if (w1 - p1 + p2 > w2 - t2) { | ~~~^~~~ DistanceMatrix.c:883:65: note: ‘p1’ 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:1374:31: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:89: 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:1374:31: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) { | ~~~~^~~~~~ DistanceMatrix.c:883:85: 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:1379:42: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1379 | sim[i] = (double)pos/((double)(ov - g2)); | ~~~~^~~~~ DistanceMatrix.c:883:81: 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:1378:10: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1378 | if (o == 1) { | ^ DistanceMatrix.c:883:105: 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; | ^ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:545:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses] 545 | x = x + (x >> 4) & 0xF0F0F0F; | ~~^~~~~~~~~~ EnumerateSequence.c: In function ‘enumerateSequence’: EnumerateSequence.c:358:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 358 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:358:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized] EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’: EnumerateSequence.c:955:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 955 | #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads) | ^~~ EnumerateSequence.c:955:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized] 381 | } else if (k == 2) { | ^ FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized] 318 | if (C[k*rc + j*r + i] >= 0) { | ~^~ FindFrameshifts.c:370:8: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized] 370 | i += B[k*rc + j*r + i]; | ~~^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 901 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41, from FindFrameshifts.c:11: /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 901 | #define eval Rf_eval | ^~~~~~~ FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here 162 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 468 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:422:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 422 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized] 432 | score += codons[lastVal*64 + val]; | ~~~~~~~^~~ GeneFinding.c: In function ‘startCodonModel’: GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 791 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreStartCodonModel’: GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 892 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘initialCodonModel’: GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 973 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreInitialCodonModel’: GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1059 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘terminationCodonModel’: GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1131 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreTerminationCodonModel’: GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1216 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘getRegion’: GeneFinding.c:1286:23: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1286 | (s == 0 && j >= 0 && j + w <= x_i.length)) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GeneFinding.c:1289:39: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1289 | seq[k] = getBaseLetterRC(x_i.ptr[j--]); | ^ GeneFinding.c: In function ‘autocorrelationModel’: GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1379 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreAutocorrelationModel’: GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1496 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘couplingModel’: GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1598 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreCouplingModel’: GeneFinding.c:1712:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1712 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘nucleotideBiasModel’: GeneFinding.c:1826:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1826 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreNucleotideBiasModel’: GeneFinding.c:1913:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1913 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘upstreamMotifModel’: GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]); | ^ GeneFinding.c: In function ‘scoreUpstreamMotifModel’: GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]); | ^ GeneFinding.c: In function ‘scoreRunLengthModel’: GeneFinding.c:2307:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2307 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘stopCodonModel’: GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2419 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘scoreStopCodonModel’: GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2520 | val = getBaseRC(x_i.ptr[j++]); | ^ GeneFinding.c: In function ‘codonFrequencies’: GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2578 | val += 4*getBaseRC(x_i.ptr[j++]); | ^ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c GetPools.c -o GetPools.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Import.c -o Import.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c InformationContent.c -o InformationContent.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IntDist.c -o IntDist.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:79:20: 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:88:20: 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:358:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 358 | *(rans + k + l*s) += 1; | ^~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c NNLS.c -o NNLS.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Order.c -o Order.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:472:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 472 | P2[i] = p2; | ~~~~~~^~~~ PairwiseAlignment.c:175:12: note: ‘p2’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:471:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 471 | P1[i] = p1; | ~~~~~~^~~~ PairwiseAlignment.c:175:7: note: ‘p1’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:476:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized] 476 | P4[i] = p4; | ~~~~~~^~~~ PairwiseAlignment.c:175:22: note: ‘p4’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c:475:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 475 | P3[i] = p3; | ~~~~~~^~~~ PairwiseAlignment.c:175:17: note: ‘p3’ was declared here 175 | int *p1, *p2, *p3, *p4; | ^~ PairwiseAlignment.c: In function ‘alignPairs’: PairwiseAlignment.c:1107:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1107 | #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads) | ^~~ PairwiseAlignment.c:1107:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] PairwiseAlignment.c:1107:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:873:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 873 | range2[0] = nucs[pos[prev]];// + 1; | ^ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 255 | SET_VECTOR_ELT(ret, i, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ PredictHEC.c:233:16: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized] 233 | states[j] = 'C'; | ~~~~~~~~~~^~~~~ PredictHEC.c:237:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized] 237 | *(rans + 3*j + 1) = E; | ~~~~~~~~~~~~^~~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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:515:12: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized] 515 | bound = s_j.length - 1; // right bound | ~~~~~~^~~~~~~~~~~~~~~~ Search.c:443:23: note: ‘s_j.length’ was declared here 443 | Chars_holder p_i, s_j; | ^~~ Search.c:443:23: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:449:9: warning: ‘maxLen’ may be used uninitialized in this function [-Wmaybe-uninitialized] 449 | int maxLen; // maximum observed length | ^~~~~~ Search.c: In function ‘searchIndex’: Search.c:969:5: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized] 969 | SET_VECTOR_ELT(ans3, k, ans); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ Search.c:201:9: warning: ‘matrices’ may be used uninitialized in this function [-Wmaybe-uninitialized] 201 | int ***matrices; | ^~~~~~~~ Search.c:208:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 208 | #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads) | ^~~ Search.c:208:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized] Search.c:208:10: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Translate.c -o Translate.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Utils.c -o Utils.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41, from Utils.c:16: Utils.c: In function ‘matchOrder’: /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized] 901 | #define eval Rf_eval | ^~~~~~~ Utils.c:333:24: note: ‘utilsPackage’ was declared here 333 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41, from Utils.c:16: /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 901 | #define eval Rf_eval | ^~~~~~~ Utils.c:333:7: note: ‘percentComplete’ was declared here 333 | SEXP percentComplete, utilsPackage; | ^~~~~~~~~~~~~~~ Utils.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized] 431 | before = *rPercentComplete; | ~~~~~~~^~~~~~~~~~~~~~~~~~~ Utils.c: In function ‘splitPartitions’: Utils.c:982:21: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized] 982 | } else if (change - j >= m && // large enough partition | ~~~~~~~^~~ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c VectorSums.c -o VectorSums.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o DECIPHER.so 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 -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)