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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 506/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.1.2  (landing page)
Erik Wright
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: devel
git_last_commit: 0eee43e
git_last_commit_date: 2024-06-01 15:10:42 -0400 (Sat, 01 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


INSTALL results for DECIPHER on palomino4

To the developers/maintainers of the DECIPHER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DECIPHER
Version: 3.1.2
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DECIPHER
StartedAt: 2024-06-09 15:52:50 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 15:54:24 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 94.3 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DECIPHER
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:437:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
  437 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:51: note: 'lGs' was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c:435:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
  435 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:46: note: 'lGp' was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0':
AlignProfiles.c:1290:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
 1290 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:819:51: note: 'lGs' was declared here
  819 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c:1288:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
 1288 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:819:46: note: 'lGp' was declared here
  819 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:388:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
  388 |                 #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(NTHREADS)
      |                         ^~~
AlignProfiles.c:81:17: note: 'subM' was declared here
   81 |         double *subM;
      |                 ^~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c AssignIndels.c -o AssignIndels.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:463:36: warning: 's1' may be used uninitialized [-Wmaybe-uninitialized]
  463 |                         if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                                ~~~~^~~~~
CalculateDeltaG.c:375:29: note: 's1' was declared here
  375 |         int i, j, k, count, s1, s2;
      |                             ^~
CalculateDeltaG.c:463:49: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized]
  463 |                         if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                                             ~~~~^~~~~
CalculateDeltaG.c:375:33: note: 's2' was declared here
  375 |         int i, j, k, count, s1, s2;
      |                                 ^~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces]
   25 |         double dH_DR[4][4] = {
      |                              ^
   26 |                 -11.5, -7.8, -7, -8.3,
      |                 {                    }
   27 |                 -10.4, -12.8, -16.3, -9.1,
      |                 {                        }
   28 |                 -8.6, -8, -9.3, -5.9,
      |                 {                   }
   29 |                 -7.8, -5.5, -9, -7.8
      |                 {
   30 |         };
      |         }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
   31 |         double dS_DR[4][4] = {
      |                              ^
   32 |                 -36.4, -21.6, -19.7, -23.9,
      |                 {                         }
   33 |                 -28.4, -31.9, -47.1, -23.5,
      |                 {                         }
   34 |                 -22.9, -17.1, -23.2, -12.3,
      |                 {                         }
   35 |                 -23.2, -13.5, -26.1, -21.9
      |                 {
   36 |         };
      |         }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
   37 |         double dH_DD[4][4] = {
      |                              ^
   38 |                 -7.9, -8.4, -7.8, -7.2,
      |                 {                     }
   39 |                 -8.5, -8, -10.6, -7.8,
      |                 {                    }
   40 |                 -8.2, -9.8, -8, -8.4,
      |                 {                   }
   41 |                 -7.2, -8.2, -8.5, -7.9
      |                 {
   42 |         };
      |         }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
   43 |         double dS_DD[4][4] = {
      |                              ^
   44 |                 -22.2, -22.4, -21, -20.4,
      |                 {                       }
   45 |                 -22.7, -19.9, -27.2, -21,
      |                 {                       }
   46 |                 -22.2, -24.4, -19.9, -22.4,
      |                 {                         }
   47 |                 -21.3, -22.2, -22.7, -22.2
      |                 {
   48 |         };
      |         }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
   49 |         double dH_RR[4][4] = {
      |                              ^
   50 |                 -6.6, -10.17, -7.65, -5.76,
      |                 {                         }
   51 |                 -10.56, -12.21, -7.95, -7.65,
      |                 {                           }
   52 |                 -13.37, -14.21, -12.21, -10.17,
      |                 {                             }
   53 |                 -8.11, -13.37, -10.56, -6.6
      |                 {
   54 |         };
      |         }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
   55 |         double dS_RR[4][4] = {
      |                              ^
   56 |                 -18.38, -26.03, -19.18, -15.67,
      |                 {                             }
   57 |                 -28.25, -30.02, -19.18, -19.18,
      |                 {                             }
   58 |                 -35.68, -34.85, -30.02, -26.03,
      |                 {                             }
   59 |                 -22.59, -35.68, -28.25, -18.38
      |                 {
   60 |         };
      |         }
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:524:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized]
  524 |                         if (minX == minY && upX == upY) {
      |                                             ~~~~^~~~~~
ChainSegments.c:490:93: note: 'upY' was declared here
  490 |                         int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                                             ^~~
ChainSegments.c:524:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized]
  524 |                         if (minX == minY && upX == upY) {
      |                                             ~~~~^~~~~~
ChainSegments.c:490:88: note: 'upX' was declared here
  490 |                         int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                                        ^~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:418:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  418 |                                         minCs[i] = minC;
      |                                         ~~~~~~~~~^~~~~~
Cluster.c:246:57: note: 'minC' was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:442:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  442 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: 'minC' was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function 'cluster':
Cluster.c:408:41: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized]
  408 |                                 #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads)
      |                                         ^~~
Cluster.c:283:17: note: 'nDiv' was declared here
  283 |         double *nDiv;
      |                 ^~~~
Cluster.c:392:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  392 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: 'minC' was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML':
ClusterML.c:1293:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized]
 1293 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
ClusterML.c:1170:17: note: 'node' was declared here
 1170 |         double *node;
      |                 ^~~~
ClusterML.c:1293:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
 1293 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
ClusterML.c:1206:14: note: 'Up' was declared here
 1206 |         int *Up;
      |              ^~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function 'clusterMP._omp_fn.0':
ClusterMP.c:165:41: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized]
  165 |                                         allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only);
      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:153:30: note: 'P' was declared here
  153 |                         int *P;
      |                              ^
ClusterMP.c:98:22: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
   98 |         int i, j, k, m, w;
      |                      ^
ClusterMP.c: In function 'clusterMP':
ClusterMP.c:140:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
  140 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:126:14: note: 'Up' was declared here
  126 |         int *Up;
      |              ^~
ClusterMP.c:140:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized]
  140 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:111:17: note: 'lengths' was declared here
  111 |         double *lengths, *score;
      |                 ^~~~~~~
ClusterMP.c:140:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized]
  140 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:112:14: note: 'nodes' was declared here
  112 |         int *nodes, *subM;
      |              ^~~~~
ClusterMP.c:140:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
  140 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:112:22: note: 'subM' was declared here
  112 |         int *nodes, *subM;
      |                      ^~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Compositions.c -o Compositions.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:1241:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized]
 1241 |                                 if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                                                    ~~~^~~~~~~~~~~~~~
Compression.c:631:26: note: 'lastTriplet' was declared here
  631 |                 int run, lastTriplet, lastCase;
      |                          ^~~~~~~~~~~
Compression.c:1011:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized]
 1011 |                                                 word = (word << 8) | (unsigned int)reorder(byte);
      |                                                        ~~~~~~^~~~~
Compression.c:544:37: note: 'word' was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                     ^~~~
Compression.c:1012:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized]
 1012 |                                                 count++;
      |                                                 ~~~~~^~
Compression.c:544:43: note: 'count' was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                           ^~~~~
Compression.c:545:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized]
  545 |                 int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                                         ^~~
Compression.c:1215:58: warning: 'lastHit' may be used uninitialized [-Wmaybe-uninitialized]
 1215 |                                                 p[c++] = (unsigned char)lastHit;
      |                                                          ^~~~~~~~~~~~~~~~~~~~~~
Compression.c:544:50: note: 'lastHit' was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                                  ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConsensusSequence.c -o ConsensusSequence.o
In function 'runsAA',
    inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3:
ConsensusSequence.c:454:50: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized]
  454 |                                 if (lastGap < (s - 2)) // ensure continuity before the run
      |                                               ~~~^~~~
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:397:30: note: 'lastPos' was declared here
  397 |         int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |                              ^~~~~~~
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:2043:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized]
 2043 |         if (tGaps && curr > 0) {
      |             ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:1930:37: note: 'curr' was declared here
 1930 |         double weight, total, prev, curr;
      |                                     ^~~~
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2186:19: warning: 'curr' may be used uninitialized [-Wmaybe-uninitialized]
 2186 |         if (tGaps && curr > 0) {
      |             ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:2073:37: note: 'curr' was declared here
 2073 |         double weight, total, prev, curr;
      |                                     ^~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces]
   70 |         double NN[4][4] = {
      |                           ^
   71 |                 -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |                 {
   72 |                 ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |                 }{
   73 |                 ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |                 }{
   74 |                 ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |                 }{
   75 |         };
      |         }
DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces]
   77 |         double PM[4][4] = {
      |                           ^
   78 |                 -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |                 {
   79 |                 ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |                 }{
   80 |                 ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |                 }{
   81 |                 ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |                 }{
   82 |         };
      |         }
DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces]
   84 |         double sMM[4][5][5][4] = {
      |                                  ^
   85 |                 0,0,0,0
      |                 {{{
   86 |                 ,1.545032445,1.254355018,1.491691514,1.329138183
      |                 }{
   87 |                 ,1.150635633,0.582415494,1.075877275,1.187937642
      |                 }{
   88 |                 ,1.203555051,1.001540513,0.864287715,0.717125848
      |                 }{
   89 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   90 |                 ,0.630005348,0.18553379,0.730763505,0.709272397
      |                 -
      |                 }},{{
   91 |                 ,0,0,0,0
      |                 }{
   92 |                 ,0.856582783,-0.143236405,0.716721488,0.603652831
      |                 }{
   93 |                 ,0.851622883,0.653168672,0.676545316,1.187937642
      |                 }{
   94 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   95 |                 ,1.231861002,0.746214538,1.087821916,0.989140748
      |                 -
      |                 }},{{
   96 |                 ,1.822113278,1.270687029,1.336192565,1.364584949
      |                 }{
   97 |                 ,0,0,0,0
      |                 }{
   98 |                 ,1.443665704,1.385046493,1.256013166,1.329138183
      |                 }{
   99 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  100 |                 ,1.478009492,0.882097231,1.20450984,1.061002478
      |                 -
      |                 }},{{
  101 |                 ,1.496720812,0.846496194,0.967868114,0.989140748
      |                 }{
  102 |                 ,0.766581547,-0.024857805,0.50754303,0.709272397
      |                 }{
  103 |                 ,0,0,0,0
      |                 }{
  104 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  105 |                 ,0.75,0.65,0.69,0.78
      |                 -
      |                 }},{{
  106 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  107 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  108 |                 ,0.76,0.65,0.69,0.78
      |                 }{
  109 |                 ,0,0,0,0
      |                 }{
  110 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  111 |                 ,1.295827995,0.84547091,0.91019099,1.256013166
      |                 }{
  112 |                 ,0.755889609,0.241428373,0.396379912,0.676545316
      |                 }{
  113 |                 ,0.99945386,0.740323132,0.435659206,0.864287715
      |                 }{
  114 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  115 |                 ,0.843147406,0.101248351,0.49063599,0.50754303
      |                 -
      |                 }},{{
  116 |                 ,0,0,0,0
      |                 }{
  117 |                 ,1.0651638,0.249934344,0.699352949,0.716721488
      |                 }{
  118 |                 ,0.871921533,0.59458138,0.396379912,1.075877275
      |                 }{
  119 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  120 |                 ,1.07531714,0.318907854,0.653287717,0.967868114
      |                 -
      |                 }},{{
  121 |                 ,1.099899195,0.730184613,0.661798984,1.336192565
      |                 }{
  122 |                 ,0,0,0,0
      |                 }{
  123 |                 ,1.45897431,1.318532145,0.91019099,1.491691514
      |                 }{
  124 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  125 |                 ,1.242135174,0.894838095,1.108555445,1.20450984
      |                 -
      |                 }},{{
  126 |                 ,0.911428974,0.524430101,0.653287717,1.087821916
      |                 }{
  127 |                 ,0.503209827,0.274849491,0.49063599,0.730763505
      |                 }{
  128 |                 ,0,0,0,0
      |                 }{
  129 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  130 |                 ,0.65,0.55,0.48,0.69
      |                 -
      |                 }},{{
  131 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  132 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  133 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  134 |                 ,0,0,0,0
      |                 }{
  135 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  136 |                 ,1.100661785,0.969784756,1.318532145,1.385046493
      |                 }{
  137 |                 ,0.565895968,-0.060347902,0.59458138,0.653168672
      |                 }{
  138 |                 ,0.782168488,0.788161238,0.740323132,1.001540513
      |                 }{
  139 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  140 |                 ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |                 -
      |                 }},{{
  141 |                 ,0,0,0,0
      |                 }{
  142 |                 ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |                 }{
  143 |                 ,0.502914193,-0.060347902,0.241428373,0.582415494
      |                 }{
  144 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  145 |                 ,0.584083861,0.258975454,0.524430101,0.846496194
      |                 -
      |                 }},{{
  146 |                 ,0.968040559,0.797499702,0.730184613,1.270687029
      |                 }{
  147 |                 ,0,0,0,0
      |                 }{
  148 |                 ,1.081040749,0.969784756,0.84547091,1.254355018
      |                 }{
  149 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  150 |                 ,1.048553951,0.728354541,0.894838095,0.882097231
      |                 -
      |                 }},{{
  151 |                 ,0.88611252,0.258975454,0.318907854,0.746214538
      |                 }{
  152 |                 ,0.239520858,-0.469855984,0.101248351,0.18553379
      |                 }{
  153 |                 ,0,0,0,0
      |                 }{
  154 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  155 |                 ,0.68,0.46,0.55,0.65
      |                 -
      |                 }},{{
  156 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  157 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  158 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  159 |                 ,0,0,0,0
      |                 }{
  160 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  161 |                 ,1.566899704,1.081040749,1.45897431,1.443665704
      |                 }{
  162 |                 ,0.976725675,0.502914193,0.871921533,0.851622883
      |                 }{
  163 |                 ,1.482046826,0.782168488,0.99945386,1.203555051
      |                 }{
  164 |                 ,0.85,0.68,0.65,0.76
      |                 }{
  165 |                 ,0.798628781,0.239520858,0.503209827,0.766581547
      |                 -
      |                 }},{{
  166 |                 ,0,0,0,0
      |                 }{
  167 |                 ,1.141098246,0.258195131,1.0651638,0.856582783
      |                 }{
  168 |                 ,0.976725675,0.565895968,0.755889609,1.150635633
      |                 }{
  169 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  170 |                 ,1.125403302,0.88611252,0.911428974,1.496720812
      |                 -
      |                 }},{{
  171 |                 ,1.68169282,0.968040559,1.099899195,1.822113278
      |                 }{
  172 |                 ,0,0,0,0
      |                 }{
  173 |                 ,1.566899704,1.100661785,1.295827995,1.545032445
      |                 }{
  174 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  175 |                 ,1.35948517,1.048553951,1.242135174,1.478009492
      |                 -
      |                 }},{{
  176 |                 ,1.125403302,0.584083861,1.07531714,1.231861002
      |                 }{
  177 |                 ,0.798628781,0.468913405,0.843147406,0.630005348
      |                 }{
  178 |                 ,0,0,0,0
      |                 }{
  179 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  180 |                 ,0.85,0.68,0.65,0.75
      |                 -
      |                 }},{{
  181 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  182 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  183 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  184 |                 ,0,0,0,0
      |                 }{
  185 |         };
      |         }}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:837:60: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized]
  837 |                                                         if (thisCycle < lastCycle) {
      |                                                            ^
DesignProbes.c:269:58: note: 'lastCycle' was declared here
  269 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                          ^~~~~~~~~
DesignProbes.c:837:60: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized]
  837 |                                                         if (thisCycle < lastCycle) {
      |                                                            ^
DesignProbes.c:269:69: note: 'thisCycle' was declared here
  269 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                                     ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Diff.c -o Diff.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:796:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  796 |                 if (!ci)
      |                 ^~
DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  799 |                         while (i < ex) {
      |                         ^~~~~
DistanceMatrix.c:818:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  818 |                 if (!cj)
      |                 ^~
DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  821 |                         while (j < ey) {
      |                         ^~~~~
DistanceMatrix.c: In function 'computeOverlap._omp_fn.0':
DistanceMatrix.c:1374:66: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:883:92: note: 'OV' was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                            ^~
DistanceMatrix.c:1374:66: warning: 'off' may be used uninitialized [-Wmaybe-uninitialized]
 1374 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:883:96: note: 'off' was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                ^~~
DistanceMatrix.c:1053:53: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized]
 1053 |                                                 two != one) {
      |                                                 ~~~~^~~~~~
DistanceMatrix.c:1028:29: note: 'one' was declared here
 1028 |                         int one, two;
      |                             ^~~
DistanceMatrix.c:1390:52: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized]
 1390 |                                                 if (o == 1) {
      |                                                    ^
DistanceMatrix.c:883:112: note: 'o' was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                                ^
DistanceMatrix.c:1393:91: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized]
 1393 |                                                         sim[i] = (double)pos/((double)(ov + count + g2));
      |                                                                                        ~~~^~~~~~~
DistanceMatrix.c:883:88: note: 'ov' was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                        ^~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:545:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  545 |         x = x + (x >> 4) & 0xF0F0F0F;
      |             ~~^~~~~~~~~~
EnumerateSequence.c: In function 'enumerateSequence':
EnumerateSequence.c:358:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized]
  358 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:317:14: note: 'mN' was declared here
  317 |         int *mN;
      |              ^~
EnumerateSequence.c:358:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized]
  358 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:318:13: note: 'tot' was declared here
  318 |         int tot; // total number of k-mers
      |             ^~~
EnumerateSequence.c: In function 'enumerateSequenceReducedAA':
EnumerateSequence.c:955:17: warning: 'mN' may be used uninitialized [-Wmaybe-uninitialized]
  955 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:907:14: note: 'mN' was declared here
  907 |         int *mN;
      |              ^~
EnumerateSequence.c:955:17: warning: 'tot' may be used uninitialized [-Wmaybe-uninitialized]
  955 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:908:13: note: 'tot' was declared here
  908 |         int tot; // total number of k-mers
      |             ^~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:464:43: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  464 |                         *rPercentComplete = floor(100*(double)(s + 1)/f_length);
      |                         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here
  160 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro 'eval'
  467 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
FindFrameshifts.c:162:14: note: 'percentComplete' was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro 'eval'
  467 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
FindFrameshifts.c:317:34: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized]
  317 |                         while (i > 0 && j > 0) {
      |                                ~~^~~
FindFrameshifts.c:135:28: note: 'I' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                            ^
FindFrameshifts.c:317:43: warning: 'J' may be used uninitialized [-Wmaybe-uninitialized]
  317 |                         while (i > 0 && j > 0) {
      |                                         ~~^~~
FindFrameshifts.c:135:31: note: 'J' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                               ^
FindFrameshifts.c:376:28: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized]
  376 |                         if (k == 1) {
      |                            ^
FindFrameshifts.c:135:34: note: 'K' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                                  ^
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:421:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  421 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:388:22: note: 'x_i.ptr' was declared here
  388 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c:431:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized]
  431 |                                 if (val < 64 && lastVal < 64)
      |                                                 ~~~~~~~~^~~~
GeneFinding.c:371:32: note: 'lastVal' was declared here
  371 |         int i, j, s, fin, val, lastVal, dicodon;
      |                                ^~~~~~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:795:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  795 |                         val = getBase(x_i.ptr[j--]);
      |                                              ^
GeneFinding.c:771:22: note: 'x_i.ptr' was declared here
  771 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:896:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  896 |                         val = getBase(x_i.ptr[j--]);
      |                                              ^
GeneFinding.c:868:22: note: 'x_i.ptr' was declared here
  868 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:951:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  951 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:928:22: note: 'x_i.ptr' was declared here
  928 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1058:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1058 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1031:22: note: 'x_i.ptr' was declared here
 1031 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1115:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1115 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1092:22: note: 'x_i.ptr' was declared here
 1092 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1215:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1215 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1188:22: note: 'x_i.ptr' was declared here
 1188 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1316:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1316 |                                                 seq[k] = getBaseLetterRC(x_i.ptr[j--]);
      |                                                                                 ^
GeneFinding.c:1252:22: note: 'x_i.ptr' was declared here
 1252 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c:1313:51: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized]
 1313 |                                 (s == 0 && j >= 0 && j + w <= x_i.length)) {
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:22: note: 'x_i.length' was declared here
 1252 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1378:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1378 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1350:22: note: 'x_i.ptr' was declared here
 1350 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1495:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1495 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1461:22: note: 'x_i.ptr' was declared here
 1461 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1597:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1597 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1573:22: note: 'x_i.ptr' was declared here
 1573 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1711:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1711 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1681:22: note: 'x_i.ptr' was declared here
 1681 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1826:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1826 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1788:22: note: 'x_i.ptr' was declared here
 1788 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1913:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1913 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1882:22: note: 'x_i.ptr' was declared here
 1882 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1992:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1992 |                                         val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
      |                                                                           ^
GeneFinding.c:1950:22: note: 'x_i.ptr' was declared here
 1950 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2092:75: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2092 |                                         val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
      |                                                                           ^
GeneFinding.c:2057:22: note: 'x_i.ptr' was declared here
 2057 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2307:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2307 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2276:22: note: 'x_i.ptr' was declared here
 2276 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2423:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2423 |                         val = getBase(x_i.ptr[j--]);
      |                                              ^
GeneFinding.c:2399:22: note: 'x_i.ptr' was declared here
 2399 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2524:46: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2524 |                         val = getBase(x_i.ptr[j--]);
      |                                              ^
GeneFinding.c:2496:22: note: 'x_i.ptr' was declared here
 2496 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2577:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2577 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2554:22: note: 'x_i.ptr' was declared here
 2554 |         Chars_holder x_i;
      |                      ^~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GetPools.c -o GetPools.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Import.c -o Import.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c InformationContent.c -o InformationContent.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IntDist.c -o IntDist.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces]
   79 |         double dH[4][4] = {
      |                           ^
   80 |                 -7.9,-8.4,-7.8,-7.2
      |                 {
   81 |                 ,-8.5,-8.0,-10.6,-7.8
      |                 }{
   82 |                 ,-8.2,-9.8,-8.0,-8.4
      |                 }{
   83 |                 ,-7.2,-8.2,-8.5,-7.9
      |                 }{
   84 |         };
      |         }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
   88 |         double dS[4][4] = {
      |                           ^
   89 |                 -22.2,-22.4,-21.0,-20.4
      |                 {
   90 |                 ,-22.7,-19.9,-27.2,-21.0
      |                 }{
   91 |                 ,-22.2,-24.4,-19.9,-22.4
      |                 }{
   92 |                 ,-21.3,-22.2,-22.7,-22.2
      |                 }{
   93 |         };
      |         }
MeltPolymer.c:406:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized]
  406 |                         SET_VECTOR_ELT(ret, s, ans);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
MeltPolymer.c:53:19: note: 'ans' was declared here
   53 |         SEXP ret, ans;
      |                   ^~~
MeltPolymer.c:358:41: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized]
  358 |                                         *(rans + k + l*s) += 1;
      |                                         ^~~~~~~~~~~~~~~~~
MeltPolymer.c:54:17: note: 'rans' was declared here
   54 |         double *rans;
      |                 ^~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MovingAverage.c -o MovingAverage.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NNLS.c -o NNLS.o
NNLS.c: In function 'NNLS':
NNLS.c:77:51: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
   77 |                                 *rPercentComplete = floor(100*((double)i + 1)/(double)l);
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NNLS.c:39:34: note: 'rPercentComplete' was declared here
   39 |         int i, j, k, before, v, *rPercentComplete;
      |                                  ^~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
                 from NNLS.c:16:
F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
NNLS.c:81:41: note: in expansion of macro 'eval'
   81 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
NNLS.c:47:14: note: 'percentComplete' was declared here
   47 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:901:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
NNLS.c:81:41: note: in expansion of macro 'eval'
   81 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
NNLS.c:47:31: note: 'utilsPackage' was declared here
   47 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Order.c -o Order.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function 'alignPair._omp_fn.0':
PairwiseAlignment.c:445:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized]
  445 |                                 p3[0] = l1;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:24: note: 'p3' was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                        ^~
PairwiseAlignment.c:446:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized]
  446 |                                 p4[0] = l2 - j1;
      |                                 ~~~~~~^~~~~~~~~
PairwiseAlignment.c:175:29: note: 'p4' was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                             ^~
PairwiseAlignment.c:449:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized]
  449 |                                 p1[0] = l2;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:14: note: 'p1' was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |              ^~
PairwiseAlignment.c:450:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized]
  450 |                                 p2[0] = l1 - i1;
      |                                 ~~~~~~^~~~~~~~~
PairwiseAlignment.c:175:19: note: 'p2' was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                   ^~
PairwiseAlignment.c: In function 'alignPairs':
PairwiseAlignment.c:1107:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
 1107 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1035:25: note: 'rPercentComplete' was declared here
 1035 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
PairwiseAlignment.c:1107:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
 1107 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1037:14: note: 'percentComplete' was declared here
 1037 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
PairwiseAlignment.c:1107:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
 1107 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1037:31: note: 'utilsPackage' was declared here
 1037 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:597:25: warning: 'leftSymbol' may be used uninitialized [-Wmaybe-uninitialized]
  597 |                         Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:485:14: note: 'leftSymbol' was declared here
  485 |         char leftSymbol, rightSymbol;
      |              ^~~~~~~~~~
PredictDBN.c:597:25: warning: 'rightSymbol' may be used uninitialized [-Wmaybe-uninitialized]
  597 |                         Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:485:26: note: 'rightSymbol' was declared here
  485 |         char leftSymbol, rightSymbol;
      |                          ^~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:38,
                 from PredictDBN.c:16:
F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/RS.h:55:25: warning: 'MI' may be used uninitialized [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:1071:9: note: in expansion of macro 'Free'
 1071 |         Free(MI);
      |         ^~~~
PredictDBN.c:236:17: note: 'MI' was declared here
  236 |         double *MI = Calloc(tot*tot, double); // initialized to zero
      |                 ^~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PredictHEC.c -o PredictHEC.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_decipher.c -o R_init_decipher.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Search.c -o Search.o
Search.c: In function 'searchIndex._omp_fn.0':
Search.c:475:75: warning: 'maxLen' may be used uninitialized [-Wmaybe-uninitialized]
  475 |                                                 if (deltaTarget >= maxSep + maxLen) {
      |                                                                    ~~~~~~~^~~~~~~~
Search.c:449:37: note: 'maxLen' was declared here
  449 |                                 int maxLen; // maximum observed length
      |                                     ^~~~~~
Search.c:443:51: warning: 's_j.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  443 |                                 Chars_holder p_i, s_j;
      |                                                   ^~~
Search.c: In function 'searchIndex':
Search.c:208:17: warning: 'sM' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:104:17: note: 'sM' was declared here
  104 |         double *sM, dS;
      |                 ^~
Search.c:208:17: warning: 'dS' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:104:21: note: 'dS' was declared here
  104 |         double *sM, dS;
      |                     ^~
Search.c:208:17: warning: 'lkup_row' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:105:14: note: 'lkup_row' was declared here
  105 |         int *lkup_row, *lkup_col;
      |              ^~~~~~~~
Search.c:208:17: warning: 'lkup_col' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:105:25: note: 'lkup_col' was declared here
  105 |         int *lkup_row, *lkup_col;
      |                         ^~~~~~~~
Search.c:208:17: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:133:25: note: 'rPercentComplete' was declared here
  133 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
Search.c:208:17: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:135:14: note: 'percentComplete' was declared here
  135 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
Search.c:208:17: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:135:31: note: 'utilsPackage' was declared here
  135 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
Search.c:208:17: warning: 'matrices' may be used uninitialized [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:201:16: note: 'matrices' was declared here
  201 |         int ***matrices;
      |                ^~~~~~~~
Search.c:943:38: warning: 'anchors' may be used uninitialized [-Wmaybe-uninitialized]
  943 |                                 int *anchor = anchors[j];
      |                                      ^~~~~~
Search.c:888:15: note: 'anchors' was declared here
  888 |         int **anchors; // pointers to anchor positions
      |               ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TerminalMismatch.c -o TerminalMismatch.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Translate.c -o Translate.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Utils.c -o Utils.o
Utils.c: In function 'splitPartitions':
Utils.c:982:35: warning: 'change' may be used uninitialized [-Wmaybe-uninitialized]
  982 |                 } else if (change - j >= m && // large enough partition
      |                            ~~~~~~~^~~
Utils.c:976:13: note: 'change' was declared here
  976 |         int change; // index before start of partition
      |             ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c VectorSums.c -o VectorSums.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)