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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DECIPHER
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:426:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
426 | 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:428:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
428 | 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:1270:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1270 | lGp *= tot;
| ~~~~^~~~~~
AlignProfiles.c:810:46: note: ‘lGp’ was declared here
810 | double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
| ^~~
AlignProfiles.c:1272:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1272 | lGs *= tot;
| ~~~~^~~~~~
AlignProfiles.c:810:51: 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:379:25: 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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:463:49: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
463 | if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
| ~~~~^~~~~
CalculateDeltaG.c:463:36: 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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces]
25 | double dH_DR[4][4] = {
| ^
26 | -11.5, -7.8, -7, -8.3,
| { }
27 | -10.4, -12.8, -16.3, -9.1,
| { }
28 | -8.6, -8, -9.3, -5.9,
| { }
29 | -7.8, -5.5, -9, -7.8
| {
30 | };
| }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
31 | double dS_DR[4][4] = {
| ^
32 | -36.4, -21.6, -19.7, -23.9,
| { }
33 | -28.4, -31.9, -47.1, -23.5,
| { }
34 | -22.9, -17.1, -23.2, -12.3,
| { }
35 | -23.2, -13.5, -26.1, -21.9
| {
36 | };
| }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
37 | double dH_DD[4][4] = {
| ^
38 | -7.9, -8.4, -7.8, -7.2,
| { }
39 | -8.5, -8, -10.6, -7.8,
| { }
40 | -8.2, -9.8, -8, -8.4,
| { }
41 | -7.2, -8.2, -8.5, -7.9
| {
42 | };
| }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
43 | double dS_DD[4][4] = {
| ^
44 | -22.2, -22.4, -21, -20.4,
| { }
45 | -22.7, -19.9, -27.2, -21,
| { }
46 | -22.2, -24.4, -19.9, -22.4,
| { }
47 | -21.3, -22.2, -22.7, -22.2
| {
48 | };
| }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
49 | double dH_RR[4][4] = {
| ^
50 | -6.6, -10.17, -7.65, -5.76,
| { }
51 | -10.56, -12.21, -7.95, -7.65,
| { }
52 | -13.37, -14.21, -12.21, -10.17,
| { }
53 | -8.11, -13.37, -10.56, -6.6
| {
54 | };
| }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
55 | double dS_RR[4][4] = {
| ^
56 | -18.38, -26.03, -19.18, -15.67,
| { }
57 | -28.25, -30.02, -19.18, -19.18,
| { }
58 | -35.68, -34.85, -30.02, -26.03,
| { }
59 | -22.59, -35.68, -28.25, -18.38
| {
60 | };
| }
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:524:49: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
524 | if (minX == minY && upX == upY) {
| ~~~~^~~~~~
ChainSegments.c:524:49: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:418:50: warning: ‘minC’ may be used uninitialized in this function [-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 in this function [-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 in this function [-Wmaybe-uninitialized]
464 | rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
| ^
Cluster.c:781:41: 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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include/Rdefines.h:38,
from ClusterML.c:16:
ClusterML.c: In function ‘clusterML’:
/home/biocbuild/bbs-3.19-bioc/R/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:1206:14: note: ‘Up’ was declared here
1206 | int *Up;
| ^~
ClusterML.c:1293:17: 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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:98:22: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
98 | int i, j, k, m, w;
| ^
ClusterMP.c:153:30: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
153 | int *P;
| ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:640:17: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
640 | free(Up);
| ^~~~~~~~
ClusterMP.c:140:17: 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:140:17: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:140:17: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:978:52: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
978 | p[c] = ((k - 1) >> 8) & 0xFF; // length of run
| ~~~^~~~
Compression.c:516:19: note: ‘k’ was declared here
516 | int i, j, k, pos;
| ^
Compression.c:1012:54: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1012 | count++;
| ~~~~~^~
Compression.c:544:43: note: ‘count’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~~
Compression.c:1011:62: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1011 | word = (word << 8) | (unsigned int)reorder(byte);
| ~~~~~~^~~~~
Compression.c:544:37: note: ‘word’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
Compression.c:1214:56: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1214 | p[c++] = rev == 0 ? 254 : 255;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:41: note: ‘rev’ was declared here
545 | int lastTemp, currTemp, rev, len, len2, thresh = 1;
| ^~~
Compression.c:558:21: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
558 | int lower = 0;
| ^~~~~
Compression.c:1241:71: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1241 | if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
| ~~~^~~~~~~~~~~~~~
Compression.c:631:26: note: ‘lastTriplet’ was declared here
631 | int run, lastTriplet, lastCase;
| ^~~~~~~~~~~
Compression.c:1031:79: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1031 | lastHit = dict[(word >> k) & 0xFF];
| ^
Compression.c:544:31: note: ‘dict’ was declared here
544 | unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
| ^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:53: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
455 | *(runs + s) += weight;
| ^~
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 in this function [-Wmaybe-uninitialized]
1771 | double *HEC, *s;
| ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2046:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2046 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2046:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1941:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1941 | int do_DBN, n, l, d;
| ^
ConsensusSequence.c:1940:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1940 | double *DBN, *s;
| ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2189:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2189 | *(rans + k) += GO*(curr*total);
| ~~~~~^~~~~~~
ConsensusSequence.c:2189:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2084:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2084 | int do_HEC, n, l, d;
| ^
ConsensusSequence.c:2083:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2083 | double *HEC, *s;
| ^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c: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:838:85: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
838 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:58: note: ‘lastCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
DesignProbes.c:838:85: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
838 | cycles += lastCycle - thisCycle;
| ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:69: note: ‘thisCycle’ was declared here
269 | int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:796:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
796 | if (!ci)
| ^~
DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
799 | while (i < ex) {
| ^~~~~
DistanceMatrix.c:818:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
818 | if (!cj)
| ^~
DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
821 | while (j < ey) {
| ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1053:53: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1053 | two != one) {
| ~~~~^~~~~~
DistanceMatrix.c:1028:29: note: ‘one’ was declared here
1028 | int one, two;
| ^~~
DistanceMatrix.c:1340:61: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1340 | if (w1 - p1 + p2 > w2 - t2) {
| ~~~~~~~~^~~~
DistanceMatrix.c:883:76: 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:1340:56: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1340 | if (w1 - p1 + p2 > w2 - t2) {
| ~~~^~~~
DistanceMatrix.c:883:72: 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:1374:66: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:96: note: ‘off’ was declared here
883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~~
DistanceMatrix.c:1374:66: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1374 | (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
| ~~~~^~~~~~
DistanceMatrix.c:883:92: note: ‘OV’ was declared here
883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~
DistanceMatrix.c:1379:91: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1379 | sim[i] = (double)pos/((double)(ov - g2));
| ~~~~^~~~~
DistanceMatrix.c:883:88: note: ‘ov’ was declared here
883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^~
DistanceMatrix.c:1378:52: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1378 | if (o == 1) {
| ^
DistanceMatrix.c:883:112: note: ‘o’ was declared here
883 | int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
| ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:545:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
545 | x = x + (x >> 4) & 0xF0F0F0F;
| ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:358:17: warning: ‘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:358:17: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:955:17: 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:955:17: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:381:35: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
381 | } else if (k == 2) {
| ^
FindFrameshifts.c:318:47: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
318 | if (C[k*rc + j*r + i] >= 0) {
| ~^~
FindFrameshifts.c:320:48: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
320 | pos = i*3 + k + 1;
| ~^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:903:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
903 | #define eval Rf_eval
| ^~~~~~~
FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here
162 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:903:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
903 | #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 in this function [-Wmaybe-uninitialized]
468 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:421:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
421 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c:432:64: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
432 | score += codons[lastVal*64 + val];
| ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:48: 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:892:48: 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:973:59: 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:1059:59: 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:1131:59: 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:1216:59: 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:1286:51: 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:1289:81: 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:1379:59: 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:1496:59: 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:1598:59: 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:1711:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1711 | val = getBaseRC(x_i.ptr[j++]);
| ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:56: 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:1913:56: 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:1990:77: 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:2090:77: 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:2307:56: 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:2419:48: 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:2520:48: 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:2578:59: 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/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces]
79 | double dH[4][4] = {
| ^
80 | -7.9,-8.4,-7.8,-7.2
| {
81 | ,-8.5,-8.0,-10.6,-7.8
| }{
82 | ,-8.2,-9.8,-8.0,-8.4
| }{
83 | ,-7.2,-8.2,-8.5,-7.9
| }{
84 | };
| }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
88 | double dS[4][4] = {
| ^
89 | -22.2,-22.4,-21.0,-20.4
| {
90 | ,-22.7,-19.9,-27.2,-21.0
| }{
91 | ,-22.2,-24.4,-19.9,-22.4
| }{
92 | ,-21.3,-22.2,-22.7,-22.2
| }{
93 | };
| }
MeltPolymer.c:358:59: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
358 | *(rans + k + l*s) += 1;
| ^~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:472:39: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
472 | P2[i] = p2;
| ~~~~~~^~~~
PairwiseAlignment.c:175:19: note: ‘p2’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:471:39: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
471 | P1[i] = p1;
| ~~~~~~^~~~
PairwiseAlignment.c:175:14: note: ‘p1’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:476:39: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
476 | P4[i] = p4;
| ~~~~~~^~~~
PairwiseAlignment.c:175:29: note: ‘p4’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c:475:39: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
475 | P3[i] = p3;
| ~~~~~~^~~~
PairwiseAlignment.c:175:24: note: ‘p3’ was declared here
175 | int *p1, *p2, *p3, *p4;
| ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1107:17: 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:1107:17: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
PairwiseAlignment.c:1107:17: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:873:85: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
873 | range2[0] = nucs[pos[prev]];// + 1;
| ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:25: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
255 | SET_VECTOR_ELT(ret, i, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:42:15: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
42 | char *states;
| ^~~~~~
PredictHEC.c:237:46: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | *(rans + 3*j + 1) = E;
| ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:515:47: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
515 | bound = s_j.length - 1; // right bound
| ~~~~~~^~~~~~~~~~~~~~~~
Search.c:443:51: note: ‘s_j.length’ was declared here
443 | Chars_holder p_i, s_j;
| ^~~
Search.c:443:51: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:449:37: warning: ‘maxLen’ may be used uninitialized in this function [-Wmaybe-uninitialized]
449 | int maxLen; // maximum observed length
| ^~~~~~
Search.c: In function ‘searchIndex’:
Search.c:969:33: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
969 | SET_VECTOR_ELT(ans3, k, ans);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Search.c:208:17: warning: ‘matrices’ 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:208:17: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include/Rdefines.h:41,
from Utils.c:16:
Utils.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:903:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
903 | #define eval Rf_eval
| ^~~~~~~
Utils.c:333:31: note: ‘utilsPackage’ was declared here
333 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
from Utils.c:16:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:903:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
903 | #define eval Rf_eval
| ^~~~~~~
Utils.c:333:14: note: ‘percentComplete’ was declared here
333 | SEXP percentComplete, utilsPackage;
| ^~~~~~~~~~~~~~~
Utils.c:431:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
431 | before = *rPercentComplete;
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
Utils.c: In function ‘splitPartitions’:
Utils.c:982:35: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized]
982 | } else if (change - j >= m && // large enough partition
| ~~~~~~~^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)
