Package: DECIPHER

Version: 2.10.2

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DECIPHER_2.10.2.tar.gz

StartedAt: 2019-04-15 23:20:35 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:26:53 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 378.8 seconds

RetCode: 0

Status:  OK

CheckDir: DECIPHER.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DECIPHER_2.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DECIPHER.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.10.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data      6.2Mb
    extdata   1.4Mb
    libs      1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
IdTaxa: no visible binding for global variable ‘L’
Undefined global functions or variables:
  L deltaHrules
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
PredictDBN         37.184  0.068  37.318
AlignSeqs          35.292  0.416  35.827
BrowseSeqs         29.440  0.092  29.668
CorrectFrameshifts 27.432  0.112  27.664
StaggerAlignment   21.416  0.188  21.659
IdTaxa             14.184  0.012  14.301
AlignTranslation   11.812  0.060  11.915
Array2Matrix        8.956  0.016   8.984
DesignArray         8.624  0.076   8.745
TileSeqs            7.108  0.000   7.138
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DECIPHER
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:401:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
         ^
AlignProfiles.c:39:39: note: ‘lGp’ was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                       ^
AlignProfiles.c:403:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
         ^
AlignProfiles.c:39:44: note: ‘lGs’ was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                            ^
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.1’:
AlignProfiles.c:1220:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
         ^
AlignProfiles.c:763:39: note: ‘lGp’ was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                       ^
AlignProfiles.c:1222:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
         ^
AlignProfiles.c:763:44: note: ‘lGs’ was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                            ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DR[4][4] = {
                       ^
CalculateFISH.c:25:23: note: (near initialization for ‘dH_DR’)
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
CalculateFISH.c:31:23: note: (near initialization for ‘dS_DR’)
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
CalculateFISH.c:37:23: note: (near initialization for ‘dH_DD’)
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
CalculateFISH.c:43:23: note: (near initialization for ‘dS_DD’)
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
CalculateFISH.c:49:23: note: (near initialization for ‘dH_RR’)
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
CalculateFISH.c:55:23: note: (near initialization for ‘dS_RR’)
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:414:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^
ChainSegments.c:414:67: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                   ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:403:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        minCol = minC;
               ^
Cluster.c:229:50: note: ‘minC’ was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:418:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       minCols[rowIndices[i]] = minC;
                              ^
Cluster.c:229:50: note: ‘minC’ was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^
Cluster.c: In function ‘cluster’:
Cluster.c:229:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:975:11: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:513:12: note: ‘k’ was declared here
  int i, j, k, pos;
            ^
Compression.c:1007:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:539:29: note: ‘count’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:1006:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:539:23: note: ‘word’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1164:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: ‘rev’ was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:626:25: warning: ‘lastCase’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1236:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:626:12: note: ‘lastTriplet’ was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:1054:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:539:17: note: ‘dict’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1938:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
  double NN[4][4] = {
                    ^
DesignProbes.c:70:20: note: (near initialization for ‘NN’)
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
DesignProbes.c:77:20: note: (near initialization for ‘PM’)
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
DesignProbes.c:84:27: note: (near initialization for ‘sMM’)
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                     ^
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                                ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:268:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
        ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:376:7: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (k==1) {
       ^
FindFrameshifts.c:372:8: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      j -= B[k*rc + j*r + i];
        ^
FindFrameshifts.c:318:22: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (C[k*rc + j*r + i] >= 0) {
                      ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
  double dH[4][4] = {
                    ^
MeltPolymer.c:79:20: note: (near initialization for ‘dH’)
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
MeltPolymer.c:88:20: note: (near initialization for ‘dS’)
MeltPolymer.c:373:33: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      slope = (*(rans + stack[0] + l*s) - *(rans + stack[pos] + l*s))/(t[stack[0]] - t[stack[pos]]);
                                 ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:244:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:244:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:327:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:352:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:352:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:428:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:454:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:454:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:543:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/Rinternals.h:1356:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
NNLS.c:82:13: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      before = *rPercentComplete;
             ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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:833:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         range2[0] = nucs[pos[prev]] + 1;
                             ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
/home/biocbuild/bbs-3.8-bioc/R/include/R_ext/RS.h:74:25: warning: ‘MI2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                         ^
PredictDBN.c:445:10: note: ‘MI2’ was declared here
  double *MI2, *rowMax, *colMax;
          ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    SET_VECTOR_ELT(ret, i, ans);
    ^
PredictHEC.c:42:8: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  char *states;
        ^
PredictHEC.c:246:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *(rans + 3*j + 2) = C/sum;
                  ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/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-3.8-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 CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (DECIPHER)

name	user	system	elapsed
AA_REDUCED	0.056	0.012	0.066
Add2DB	0.336	0.028	0.381
AdjustAlignment	0.352	0.012	0.379
AlignDB	1.604	0.056	1.701
AlignProfiles	1.304	0.012	1.352
AlignSeqs	35.292	0.416	35.827
AlignSynteny	3.732	0.012	3.794
AlignTranslation	11.812	0.060	11.915
AmplifyDNA	0.004	0.000	0.004
Array2Matrix	8.956	0.016	8.984
BrowseDB	0.040	0.000	0.043
BrowseSeqs	29.440	0.092	29.668
CalculateEfficiencyArray	0.020	0.000	0.021
CalculateEfficiencyFISH	0.008	0.000	0.008
CalculateEfficiencyPCR	0.008	0.000	0.008
Codec	1.076	0.000	1.078
ConsensusSequence	0.292	0.000	0.294
CorrectFrameshifts	27.432	0.112	27.664
CreateChimeras	1.296	0.000	1.299
DB2Seqs	0.012	0.024	0.056
DesignArray	8.624	0.076	8.745
DesignPrimers	0.000	0.000	0.001
DesignProbes	0.000	0.000	0.001
DesignSignatures	0.000	0.000	0.001
DigestDNA	0.224	0.004	0.225
Disambiguate	0.064	0.000	0.066
DistanceMatrix	0.040	0.000	0.041
FindChimeras	0.096	0.000	0.095
FindSynteny	2.316	0.000	2.316
FormGroups	0.088	0.008	0.096
HEC_MI	0.284	0.000	0.285
IdClusters	2.380	0.036	2.430
IdConsensus	1.144	0.000	1.153
IdLengths	0.028	0.000	0.026
IdTaxa	14.184	0.012	14.301
IdentifyByRank	0.048	0.000	0.050
LearnTaxa	4.244	0.124	4.370
MIQS	0.032	0.000	0.033
MODELS	0	0	0
MaskAlignment	0.932	0.020	0.955
MeltDNA	0.060	0.004	0.083
NNLS	0.004	0.000	0.004
OrientNucleotides	1.468	0.000	1.479
PFASUM	0.004	0.004	0.011
PredictDBN	37.184	0.068	37.318
PredictHEC	0.412	0.016	0.429
RESTRICTION_ENZYMES	0.008	0.000	0.005
ReadDendrogram	0.032	0.000	0.032
RemoveGaps	0.012	0.004	0.017
SearchDB	0.056	0.000	0.057
Seqs2DB	0.156	0.004	0.158
StaggerAlignment	21.416	0.188	21.659
Synteny-class	3.460	0.008	3.528
Taxa-class	3.004	0.008	3.030
TerminalChar	0.016	0.000	0.018
TileSeqs	7.108	0.000	7.138
TrainingSet_16S	3.352	0.024	3.378
TrimDNA	0.100	0.000	0.099
WriteDendrogram	0.008	0.000	0.008
deltaGrules	0.012	0.000	0.015
deltaHrules	0.020	0.004	0.027
deltaSrules	0.076	0.000	0.079