BioC 3.2: CHECK report for DECIPHER on linux1.bioconductor.org

Package: DECIPHER

Version: 1.16.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.16.0.tar.gz

StartedAt: 2015-10-27 02:48:23 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:53:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 335.0 seconds

RetCode: 0

Status:  OK

CheckDir: DECIPHER.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DECIPHER.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.16.0’
* 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 ... [18s/18s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       3.6Mb
    extdata   1.5Mb
* 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 loading without being on the library search path ... 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’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [541s/217s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
CorrectFrameshifts 151.063  0.464  55.396
AlignTranslation   114.147  0.310  40.295
StaggerAlignment   112.188  0.367  42.482
AlignSeqs           78.086  0.301  26.295
OrientNucleotides   13.804  0.082   4.203
Array2Matrix        12.702  0.036   4.474
DesignArray         12.486  0.074   4.270
TileSeqs             9.376  0.003   9.382
AlignSynteny         8.100  0.777   5.402
BrowseSeqs           6.079  0.023   6.105
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AppendXStringSets.c -o AppendXStringSets.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
   -11.5, -7.8, -7, -8.3,
   ^
CalculateFISH.c:26:3: warning: (near initialization for ‘dH_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
   -36.4, -21.6, -19.7, -23.9,
   ^
CalculateFISH.c:32:3: warning: (near initialization for ‘dS_DR[0]’) [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9, -8.4, -7.8, -7.2,
   ^
CalculateFISH.c:38:3: warning: (near initialization for ‘dH_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2, -22.4, -21, -20.4,
   ^
CalculateFISH.c:44:3: warning: (near initialization for ‘dS_DD[0]’) [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
   -6.6, -10.17, -7.65, -5.76,
   ^
CalculateFISH.c:50:3: warning: (near initialization for ‘dH_RR[0]’) [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
   -18.38, -26.03, -19.18, -15.67,
   ^
CalculateFISH.c:56:3: warning: (near initialization for ‘dS_RR[0]’) [-Wmissing-braces]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘indexByContig’:
ChainSegments.c:79:6: warning: unused variable ‘n’ [-Wunused-variable]
  int n = length(widths);
      ^
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:404:72: 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:452:8: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (upX) { // new chain is last
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:281:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterNJ.c:195:62: note: ‘minC’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                              ^
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterNJ.c:195:56: note: ‘minR’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                        ^
ClusterNJ.c: In function ‘clusterNJ’:
ClusterNJ.c:491:9: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
         ^
ClusterNJ.c:491:9: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterNJ.c:487:29: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                             ^
ClusterNJ.c:492:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:200:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                              ^
ClusterUPGMA.c:199:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                        ^
ClusterUPGMA.c: In function ‘clusterUPGMA’:
ClusterUPGMA.c:430:9: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
         ^
ClusterUPGMA.c:430:9: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterUPGMA.c:426:29: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                             ^
ClusterUPGMA.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:1748:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1915:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2040:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   ^
DesignProbes.c:71:3: warning: (near initialization for ‘NN[0]’) [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   ^
DesignProbes.c:78:3: warning: (near initialization for ‘PM[0]’) [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
   0,0,0,0
   ^
DesignProbes.c:85:3: warning: (near initialization for ‘sMM[0]’) [-Wmissing-braces]
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 -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘enumerateGappedSequence’:
EnumerateSequence.c:267:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
EnumerateSequence.c: In function ‘enumerateGappedSequenceAA’:
EnumerateSequence.c:364:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:160:9: warning: unused variable ‘soFar’ [-Wunused-variable]
  double soFar;
         ^
FindFrameshifts.c:319:8: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      d = k - C[k*rc + j*r + i];
        ^
FindFrameshifts.c:317:22: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    while (i > 0 && j > 0) {
                      ^
FindFrameshifts.c:317:13: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    while (i > 0 && j > 0) {
             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9,-8.4,-7.8,-7.2
   ^
MeltPolymer.c:80:3: warning: (near initialization for ‘dH[0]’) [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2,-22.4,-21.0,-20.4
   ^
MeltPolymer.c:89:3: warning: (near initialization for ‘dS[0]’) [-Wmissing-braces]
MeltPolymer.c:54:10: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *rans;
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c SubsetXStringSet.c -o SubsetXStringSet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AppendXStringSets.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o Order.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o SubsetXStringSet.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
** inst
** preparing 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
Add2DB	0.253	0.008	0.261
AdjustAlignment	0.354	0.020	0.274
AlignDB	2.184	0.063	2.158
AlignProfiles	1.883	0.071	1.679
AlignSeqs	78.086	0.301	26.295
AlignSynteny	8.100	0.777	5.402
AlignTranslation	114.147	0.310	40.295
AmplifyDNA	0.001	0.000	0.005
Array2Matrix	12.702	0.036	4.474
BrowseDB	0.022	0.000	0.022
BrowseSeqs	6.079	0.023	6.105
CalculateEfficiencyArray	0.015	0.000	0.014
CalculateEfficiencyFISH	0.007	0.000	0.008
CalculateEfficiencyPCR	0.006	0.000	0.007
ConsensusSequence	0.01	0.00	0.01
CorrectFrameshifts	151.063	0.464	55.396
CreateChimeras	2.108	0.025	1.467
DB2Seqs	0.020	0.007	0.026
DesignArray	12.486	0.074	4.270
DesignPrimers	0.001	0.000	0.001
DesignProbes	0.002	0.000	0.001
DesignSignatures	0.002	0.000	0.002
DigestDNA	0.385	0.033	0.288
Disambiguate	0.063	0.000	0.063
DistanceMatrix	0.104	0.034	0.058
FindChimeras	0.057	0.012	0.069
FindSynteny	1.690	0.004	1.694
FormGroups	0.140	0.000	0.139
HEC_MI	0.204	0.004	0.208
IdClusters	0.950	0.024	0.361
IdConsensus	0.947	0.012	0.959
IdLengths	0.02	0.00	0.02
IdentifyByRank	0.019	0.000	0.019
MIQS	0.004	0.000	0.006
MODELS	0.001	0.000	0.000
MaskAlignment	0.591	0.008	0.598
MeltDNA	0.049	0.004	0.053
NNLS	0.197	0.018	0.071
OrientNucleotides	13.804	0.082	4.203
PredictHEC	0.326	0.008	0.334
RESTRICTION_ENZYMES	0.003	0.000	0.002
SearchDB	0.055	0.000	0.055
Seqs2DB	0.329	0.004	0.333
StaggerAlignment	112.188	0.367	42.482
Synteny-class	3.647	0.004	3.652
TerminalChar	0.033	0.000	0.033
TileSeqs	9.376	0.003	9.382
deltaGrules	0.009	0.000	0.010
deltaHrules	0.019	0.000	0.019
deltaSrules	0.039	0.004	0.043