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### Running command:
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### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL DECIPHER
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:424:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
424 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:46: note: 'lGp' was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c:426:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
426 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:61:51: note: 'lGs' was declared here
61 | double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0':
AlignProfiles.c:1266:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
1266 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:46: note: 'lGp' was declared here
808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1268:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
1268 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:808:51: note: 'lGs' was declared here
808 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:378:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
378 | #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
| ^~~
AlignProfiles.c:81:17: note: 'subM' was declared here
81 | double *subM;
| ^~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:463:49: 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;
| ^~
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;
| ^~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces]
25 | double dH_DR[4][4] = {
| ^
26 | -11.5, -7.8, -7, -8.3,
| { }
27 | -10.4, -12.8, -16.3, -9.1,
| { }
28 | -8.6, -8, -9.3, -5.9,
| { }
29 | -7.8, -5.5, -9, -7.8
| {
30 | };
| }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
31 | double dS_DR[4][4] = {
| ^
32 | -36.4, -21.6, -19.7, -23.9,
| { }
33 | -28.4, -31.9, -47.1, -23.5,
| { }
34 | -22.9, -17.1, -23.2, -12.3,
| { }
35 | -23.2, -13.5, -26.1, -21.9
| {
36 | };
| }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
37 | double dH_DD[4][4] = {
| ^
38 | -7.9, -8.4, -7.8, -7.2,
| { }
39 | -8.5, -8, -10.6, -7.8,
| { }
40 | -8.2, -9.8, -8, -8.4,
| { }
41 | -7.2, -8.2, -8.5, -7.9
| {
42 | };
| }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
43 | double dS_DD[4][4] = {
| ^
44 | -22.2, -22.4, -21, -20.4,
| { }
45 | -22.7, -19.9, -27.2, -21,
| { }
46 | -22.2, -24.4, -19.9, -22.4,
| { }
47 | -21.3, -22.2, -22.7, -22.2
| {
48 | };
| }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
49 | double dH_RR[4][4] = {
| ^
50 | -6.6, -10.17, -7.65, -5.76,
| { }
51 | -10.56, -12.21, -7.95, -7.65,
| { }
52 | -13.37, -14.21, -12.21, -10.17,
| { }
53 | -8.11, -13.37, -10.56, -6.6
| {
54 | };
| }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
55 | double dS_RR[4][4] = {
| ^
56 | -18.38, -26.03, -19.18, -15.67,
| { }
57 | -28.25, -30.02, -19.18, -19.18,
| { }
58 | -35.68, -34.85, -30.02, -26.03,
| { }
59 | -22.59, -35.68, -28.25, -18.38
| {
60 | };
| }
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:500:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized]
500 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:466:93: note: 'upY' was declared here
466 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
ChainSegments.c:500:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized]
500 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:466:88: note: 'upX' was declared here
466 | int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
| ^~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:418:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
418 | minCs[i] = minC;
| ~~~~~~~~~^~~~~~
Cluster.c:246:57: note: 'minC' was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:442:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
442 | minCols[rowIndices[i]] = minC;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: 'minC' was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c: In function 'cluster':
Cluster.c:464:66: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
464 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
| ^
Cluster.c:246:57: note: 'minC' was declared here
246 | int k, dobj, clusterNum, minRow, minCol, index, minC, met;
| ^~~~
Cluster.c:793:47: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized]
793 | nDiv[i] = nDiv[i + 1];
| ~~~~^~~~~~~
Cluster.c:283:17: note: 'nDiv' was declared here
283 | double *nDiv;
| ^~~~
In file included from F:/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:41,
from Cluster.c:11:
F:/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:894:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
894 | #define eval Rf_eval
| ^~~~~~~
Cluster.c:250:36: note: 'utilsPackage' was declared here
250 | SEXP ans, percentComplete, utilsPackage;
| ^~~~~~~~~~~~
F:/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:894:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
894 | #define eval Rf_eval
| ^~~~~~~
Cluster.c:250:19: note: 'percentComplete' was declared here
250 | SEXP ans, percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
Cluster.c:855:43: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized]
855 | *rPercentComplete = floor(100*soFar/total);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Cluster.c:249:23: note: 'total' was declared here
249 | double soFar, total, minHeight, *cut, *rans, *distanceMatrix, minH;
| ^~~~~
Cluster.c:860:40: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
860 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
Cluster.c:248:25: note: 'rPercentComplete' was declared here
248 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
Cluster.c:841:52: warning: 'minCols' may be used uninitialized [-Wmaybe-uninitialized]
841 | if (minCols[rowIndices[j]] >= 0) {
| ^
Cluster.c:277:14: note: 'minCols' was declared here
277 | int *minCols;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o
In file included from F:/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:38,
from ClusterML.c:11:
F:/biocbuild/bbs-3.18-bioc/R/include/R_ext/RS.h: In function 'clusterML':
F:/biocbuild/bbs-3.18-bioc/R/include/R_ext/RS.h:55:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
55 | #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
| ^~~~~~~~~~
ClusterML.c:1126:14: note: 'Up' was declared here
1126 | int *Up;
| ^~
ClusterML.c:1210:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized]
1210 | #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
| ^~~
ClusterML.c:1090:17: note: 'node' was declared here
1090 | double *node;
| ^~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function 'clusterMP._omp_fn.0':
ClusterMP.c:98:22: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
98 | int i, j, k, m, w;
| ^
ClusterMP.c:271:57: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized]
271 | allStates(R, P, S, c, n, c, k - 1, c, n, 0, 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:151:30: note: 'P' was declared here
151 | int *P;
| ^
ClusterMP.c: In function 'clusterMP':
ClusterMP.c:139:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
139 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:126:14: note: 'Up' was declared here
126 | int *Up;
| ^~
ClusterMP.c:139:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
139 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:112:22: note: 'subM' was declared here
112 | int *nodes, *subM;
| ^~~~
ClusterMP.c:139:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized]
139 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:112:14: note: 'nodes' was declared here
112 | int *nodes, *subM;
| ^~~~~
ClusterMP.c:139:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized]
139 | #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
| ^~~
ClusterMP.c:111:17: note: 'lengths' was declared here
111 | double *lengths, *score;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:993:35: warning: 'k' may be used uninitialized [-Wmaybe-uninitialized]
993 | j += k;
| ~~^~~~
Compression.c:516:19: note: 'k' was declared here
516 | int i, j, k, pos;
| ^
Compression.c:1010:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized]
1010 | count++;
| ~~~~~^~
Compression.c:542:43: note: 'count' was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:1009:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized]
1009 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:542:37: note: 'word' was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:543:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized]
543 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:1239:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized]
1239 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:629:26: note: 'lastTriplet' was declared here
629 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1086:61: warning: 'dict' may be used uninitialized [-Wmaybe-uninitialized]
1086 | dict[word] = j;
| ^
Compression.c:542:31: note: 'dict' was declared here
542 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfile':
ConsensusSequence.c:1578:17: warning: 'DBN' may be used uninitialized [-Wmaybe-uninitialized]
1578 | double *DBN, *s;
| ^~~
In function 'runsAA',
inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3:
ConsensusSequence.c:455:41: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized]
455 | *(runs + s) += weight;
| ^~~~~~~~~~~
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:1771:17: warning: 'HEC' may be used uninitialized [-Wmaybe-uninitialized]
1771 | double *HEC, *s;
| ^~~
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:2046:48: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized]
2046 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:1930:37: note: 'curr' was declared here
1930 | double weight, total, prev, curr;
| ^~~~
ConsensusSequence.c:1941:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized]
1941 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:1940:17: warning: 'DBN' may be used uninitialized [-Wmaybe-uninitialized]
1940 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2189:48: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized]
2189 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2073:37: note: 'curr' was declared here
2073 | double weight, total, prev, curr;
| ^~~~
ConsensusSequence.c:2084:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized]
2084 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2083:17: warning: 'HEC' may be used uninitialized [-Wmaybe-uninitialized]
2083 | double *HEC, *s;
| ^~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces]
70 | double NN[4][4] = {
| ^
71 | -0.816507461,-2.5401714,-1.647430026,-1.184658548
| {
72 | ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
| }{
73 | ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
| }{
74 | ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
| }{
75 | };
| }
DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces]
77 | double PM[4][4] = {
| ^
78 | -0.141370102,-0.439805276,-0.285236035,-0.205111781
| {
79 | ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
| }{
80 | ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
| }{
81 | ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
| }{
82 | };
| }
DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces]
84 | double sMM[4][5][5][4] = {
| ^
85 | 0,0,0,0
| {{{
86 | ,1.545032445,1.254355018,1.491691514,1.329138183
| }{
87 | ,1.150635633,0.582415494,1.075877275,1.187937642
| }{
88 | ,1.203555051,1.001540513,0.864287715,0.717125848
| }{
89 | ,0.75,0.65,0.69,0.78
| }{
90 | ,0.630005348,0.18553379,0.730763505,0.709272397
| -
| }},{{
91 | ,0,0,0,0
| }{
92 | ,0.856582783,-0.143236405,0.716721488,0.603652831
| }{
93 | ,0.851622883,0.653168672,0.676545316,1.187937642
| }{
94 | ,0.75,0.65,0.69,0.78
| }{
95 | ,1.231861002,0.746214538,1.087821916,0.989140748
| -
| }},{{
96 | ,1.822113278,1.270687029,1.336192565,1.364584949
| }{
97 | ,0,0,0,0
| }{
98 | ,1.443665704,1.385046493,1.256013166,1.329138183
| }{
99 | ,0.75,0.65,0.69,0.78
| }{
100 | ,1.478009492,0.882097231,1.20450984,1.061002478
| -
| }},{{
101 | ,1.496720812,0.846496194,0.967868114,0.989140748
| }{
102 | ,0.766581547,-0.024857805,0.50754303,0.709272397
| }{
103 | ,0,0,0,0
| }{
104 | ,0.75,0.65,0.69,0.78
| }{
105 | ,0.75,0.65,0.69,0.78
| -
| }},{{
106 | ,0.75,0.65,0.69,0.78
| }{
107 | ,0.75,0.65,0.69,0.78
| }{
108 | ,0.76,0.65,0.69,0.78
| }{
109 | ,0,0,0,0
| }{
110 | ,0,0,0,0
| -
| }}},{{{
111 | ,1.295827995,0.84547091,0.91019099,1.256013166
| }{
112 | ,0.755889609,0.241428373,0.396379912,0.676545316
| }{
113 | ,0.99945386,0.740323132,0.435659206,0.864287715
| }{
114 | ,0.65,0.55,0.48,0.69
| }{
115 | ,0.843147406,0.101248351,0.49063599,0.50754303
| -
| }},{{
116 | ,0,0,0,0
| }{
117 | ,1.0651638,0.249934344,0.699352949,0.716721488
| }{
118 | ,0.871921533,0.59458138,0.396379912,1.075877275
| }{
119 | ,0.65,0.56,0.49,0.69
| }{
120 | ,1.07531714,0.318907854,0.653287717,0.967868114
| -
| }},{{
121 | ,1.099899195,0.730184613,0.661798984,1.336192565
| }{
122 | ,0,0,0,0
| }{
123 | ,1.45897431,1.318532145,0.91019099,1.491691514
| }{
124 | ,0.65,0.56,0.49,0.69
| }{
125 | ,1.242135174,0.894838095,1.108555445,1.20450984
| -
| }},{{
126 | ,0.911428974,0.524430101,0.653287717,1.087821916
| }{
127 | ,0.503209827,0.274849491,0.49063599,0.730763505
| }{
128 | ,0,0,0,0
| }{
129 | ,0.65,0.55,0.48,0.69
| }{
130 | ,0.65,0.55,0.48,0.69
| -
| }},{{
131 | ,0.65,0.56,0.49,0.69
| }{
132 | ,0.65,0.56,0.49,0.69
| }{
133 | ,0.65,0.55,0.48,0.69
| }{
134 | ,0,0,0,0
| }{
135 | ,0,0,0,0
| -
| }}},{{{
136 | ,1.100661785,0.969784756,1.318532145,1.385046493
| }{
137 | ,0.565895968,-0.060347902,0.59458138,0.653168672
| }{
138 | ,0.782168488,0.788161238,0.740323132,1.001540513
| }{
139 | ,0.68,0.46,0.55,0.65
| }{
140 | ,0.468913405,-0.469855984,0.274849491,-0.024857805
| -
| }},{{
141 | ,0,0,0,0
| }{
142 | ,0.258195131,-0.70438632,0.249934344,-0.143236405
| }{
143 | ,0.502914193,-0.060347902,0.241428373,0.582415494
| }{
144 | ,0.68,0.47,0.56,0.65
| }{
145 | ,0.584083861,0.258975454,0.524430101,0.846496194
| -
| }},{{
146 | ,0.968040559,0.797499702,0.730184613,1.270687029
| }{
147 | ,0,0,0,0
| }{
148 | ,1.081040749,0.969784756,0.84547091,1.254355018
| }{
149 | ,0.68,0.47,0.56,0.65
| }{
150 | ,1.048553951,0.728354541,0.894838095,0.882097231
| -
| }},{{
151 | ,0.88611252,0.258975454,0.318907854,0.746214538
| }{
152 | ,0.239520858,-0.469855984,0.101248351,0.18553379
| }{
153 | ,0,0,0,0
| }{
154 | ,0.68,0.46,0.55,0.65
| }{
155 | ,0.68,0.46,0.55,0.65
| -
| }},{{
156 | ,0.68,0.47,0.56,0.65
| }{
157 | ,0.68,0.47,0.56,0.65
| }{
158 | ,0.68,0.46,0.55,0.65
| }{
159 | ,0,0,0,0
| }{
160 | ,0,0,0,0
| -
| }}},{{{
161 | ,1.566899704,1.081040749,1.45897431,1.443665704
| }{
162 | ,0.976725675,0.502914193,0.871921533,0.851622883
| }{
163 | ,1.482046826,0.782168488,0.99945386,1.203555051
| }{
164 | ,0.85,0.68,0.65,0.76
| }{
165 | ,0.798628781,0.239520858,0.503209827,0.766581547
| -
| }},{{
166 | ,0,0,0,0
| }{
167 | ,1.141098246,0.258195131,1.0651638,0.856582783
| }{
168 | ,0.976725675,0.565895968,0.755889609,1.150635633
| }{
169 | ,0.85,0.68,0.65,0.75
| }{
170 | ,1.125403302,0.88611252,0.911428974,1.496720812
| -
| }},{{
171 | ,1.68169282,0.968040559,1.099899195,1.822113278
| }{
172 | ,0,0,0,0
| }{
173 | ,1.566899704,1.100661785,1.295827995,1.545032445
| }{
174 | ,0.85,0.68,0.65,0.75
| }{
175 | ,1.35948517,1.048553951,1.242135174,1.478009492
| -
| }},{{
176 | ,1.125403302,0.584083861,1.07531714,1.231861002
| }{
177 | ,0.798628781,0.468913405,0.843147406,0.630005348
| }{
178 | ,0,0,0,0
| }{
179 | ,0.85,0.68,0.65,0.75
| }{
180 | ,0.85,0.68,0.65,0.75
| -
| }},{{
181 | ,0.85,0.68,0.65,0.75
| }{
182 | ,0.85,0.68,0.65,0.75
| }{
183 | ,0.85,0.68,0.65,0.75
| }{
184 | ,0,0,0,0
| }{
185 | };
| }}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:836:77: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized]
836 | cycles += 4 + lastCycle - thisCycle;
| ~~^~~~~~~~~~~
DesignProbes.c:267:58: note: 'lastCycle' was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:834:85: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized]
834 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:69: note: 'thisCycle' was declared here
267 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:794:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
794 | if (!ci)
| ^~
DistanceMatrix.c:797:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
797 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:816:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
816 | if (!cj)
| ^~
DistanceMatrix.c:819:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
819 | while (j < ey) {
| ^~~~~
DistanceMatrix.c: In function 'similarities._omp_fn.0':
DistanceMatrix.c:1040:61: warning: 'off' may be used uninitialized [-Wmaybe-uninitialized]
1040 | (w1 <= w2[i] && (double)(OV + off)/(double)w2[i] < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:881:49: note: 'off' was declared here
881 | int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
| ^~~
DistanceMatrix.c:1040:61: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized]
1040 | (w1 <= w2[i] && (double)(OV + off)/(double)w2[i] < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:881:45: note: 'OV' was declared here
881 | int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
| ^~
DistanceMatrix.c:1059:82: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized]
1059 | rans[i] = (double)s/((double)(ov + count + g2));
| ~~~^~~~~~~
DistanceMatrix.c:881:41: note: 'ov' was declared here
881 | int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
| ^~
DistanceMatrix.c:1044:44: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized]
1044 | if (o == 1) {
| ^
DistanceMatrix.c:881:65: note: 'o' was declared here
881 | int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
| ^
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:321:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
321 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:381:35: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized]
381 | } else if (k == 2) {
| ^
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;
| ^
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: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;
| ^
In file included from F:/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
F:/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:894:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
894 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
F:/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:894:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
894 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:14: note: 'percentComplete' was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:40: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
468 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here
160 | int before, v, *rPercentComplete;
| ^~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:431:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized]
431 | if (val < 64 && lastVal < 64)
| ~~~~~~~~^~~~
GeneFinding.c:371:32: note: 'lastVal' was declared here
371 | int i, j, s, fin, val, lastVal, dicodon;
| ^~~~~~~
GeneFinding.c:421:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
421 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:388:22: note: 'x_i.ptr' was declared here
388 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:791:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
791 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:771:22: note: 'x_i.ptr' was declared here
771 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:892:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
892 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:868:22: note: 'x_i.ptr' was declared here
868 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:972:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
972 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:928:22: note: 'x_i.ptr' was declared here
928 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1058:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1058 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1031:22: note: 'x_i.ptr' was declared here
1031 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1130:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1130 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1092:22: note: 'x_i.ptr' was declared here
1092 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1215:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1215 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1188:22: note: 'x_i.ptr' was declared here
1188 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1285:37: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized]
1285 | if ((s == 1 && j < x_i.length && j - w + 1 >= 0) ||
| ~~~~~~~^~~~~~~~~~~~~~~~~
GeneFinding.c:1252:22: note: 'x_i.length' was declared here
1252 | Chars_holder x_i;
| ^~~
GeneFinding.c:1289:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1289 | seq[k] = getBaseLetterRC(x_i.ptr[j--]);
| ^
GeneFinding.c:1252:22: note: 'x_i.ptr' was declared here
1252 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1378:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1378 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1350:22: note: 'x_i.ptr' was declared here
1350 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1495:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1495 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1461:22: note: 'x_i.ptr' was declared here
1461 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1597:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1597 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1573:22: note: 'x_i.ptr' was declared here
1573 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1711:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1711 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1681:22: note: 'x_i.ptr' was declared here
1681 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1826:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1826 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1788:22: note: 'x_i.ptr' was declared here
1788 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1913:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1913 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:1882:22: note: 'x_i.ptr' was declared here
1882 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1990:77: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
1990 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c:1950:22: note: 'x_i.ptr' was declared here
1950 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2090:77: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2090 | val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
| ^
GeneFinding.c:2057:22: note: 'x_i.ptr' was declared here
2057 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2307:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2307 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2276:22: note: 'x_i.ptr' was declared here
2276 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2419:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2419 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2399:22: note: 'x_i.ptr' was declared here
2399 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2520:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2520 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2496:22: note: 'x_i.ptr' was declared here
2496 | Chars_holder x_i;
| ^~~
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2577:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
2577 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:2554:22: note: 'x_i.ptr' was declared here
2554 | Chars_holder x_i;
| ^~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces]
79 | double dH[4][4] = {
| ^
80 | -7.9,-8.4,-7.8,-7.2
| {
81 | ,-8.5,-8.0,-10.6,-7.8
| }{
82 | ,-8.2,-9.8,-8.0,-8.4
| }{
83 | ,-7.2,-8.2,-8.5,-7.9
| }{
84 | };
| }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
88 | double dS[4][4] = {
| ^
89 | -22.2,-22.4,-21.0,-20.4
| {
90 | ,-22.7,-19.9,-27.2,-21.0
| }{
91 | ,-22.2,-24.4,-19.9,-22.4
| }{
92 | ,-21.3,-22.2,-22.7,-22.2
| }{
93 | };
| }
MeltPolymer.c:54:17: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized]
54 | double *rans;
| ^~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function 'alignPair._omp_fn.0':
PairwiseAlignment.c:469:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized]
469 | P2[i] = p2;
| ~~~~~~^~~~
PairwiseAlignment.c:172:19: note: 'p2' was declared here
172 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:468:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized]
468 | P1[i] = p1;
| ~~~~~~^~~~
PairwiseAlignment.c:172:14: note: 'p1' was declared here
172 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:473:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized]
473 | P4[i] = p4;
| ~~~~~~^~~~
PairwiseAlignment.c:172:29: note: 'p4' was declared here
172 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:472:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized]
472 | P3[i] = p3;
| ~~~~~~^~~~
PairwiseAlignment.c:172:24: note: 'p3' was declared here
172 | int *p1, *p2, *p3, *p4;
| ^~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:255:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized]
255 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:49:19: note: 'ans' was declared here
49 | SEXP ret, ans;
| ^~~
PredictHEC.c:233:51: warning: 'states' may be used uninitialized [-Wmaybe-uninitialized]
233 | states[j] = 'C';
| ~~~~~~~~~~^~~~~
PredictHEC.c:42:15: note: 'states' was declared here
42 | char *states;
| ^~~~~~
PredictHEC.c:236:40: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized]
236 | *(rans + 3*j) = H;
| ~~~~~~^~~~~~
PredictHEC.c:41:31: note: 'rans' was declared here
41 | double H, E, C, sum, *rans;
| ^~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.c -o Utils.o
Utils.c: In function 'intMatchSelfOnce':
Utils.c:654:28: warning: variable 'start' set but not used [-Wunused-but-set-variable]
654 | int i, j, k, temp, start = 0;
| ^~~~~
Utils.c: In function 'matchOverlap._omp_fn.0':
Utils.c:823:53: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized]
823 | two != one) {
| ~~~~^~~~~~
Utils.c:798:29: note: 'one' was declared here
798 | int one, two;
| ^~~
Utils.c: In function 'splitPartitions':
Utils.c:1315:35: warning: 'change' may be used uninitialized [-Wmaybe-uninitialized]
1315 | } else if (change - j >= m && // large enough partition
| ~~~~~~~^~~
Utils.c:1309:13: note: 'change' was declared here
1309 | int change; // index before start of partition
| ^~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)
