DECIPHER 1.16.0
Erik Wright
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DECIPHER | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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###
### Running command:
###
### rm -rf DECIPHER.buildbin-libdir DECIPHER.Rcheck && mkdir DECIPHER.buildbin-libdir DECIPHER.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.16.0.tar.gz >DECIPHER.Rcheck\00install.out 2>&1 && cp DECIPHER.Rcheck\00install.out DECIPHER-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_1.16.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
data 2.5Mb
doc 3.8Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64/DECIPHER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [140s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
StaggerAlignment 32.69 5.82 30.27
CorrectFrameshifts 33.51 4.58 32.11
AlignSeqs 22.67 5.83 20.95
AlignTranslation 18.86 2.89 16.39
DesignArray 11.70 0.29 2.61
Array2Matrix 10.95 0.23 2.57
TileSeqs 8.49 0.00 8.49
BrowseSeqs 5.64 0.08 5.72
AlignSynteny 4.41 0.93 5.27
** running examples for arch 'x64' ... [145s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CorrectFrameshifts 29.66 4.03 31.30
StaggerAlignment 27.13 6.29 30.60
AlignSeqs 15.21 5.86 18.17
AlignTranslation 17.00 2.42 17.59
TileSeqs 10.61 0.02 10.62
Array2Matrix 9.36 0.38 2.62
DesignArray 9.37 0.28 2.59
BrowseSeqs 6.74 0.03 6.77
AlignSynteny 5.04 0.78 5.74
* 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
'C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'DECIPHER' ...
** libs
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:63:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c: In function 'alignProfilesAA':
AlignProfiles.c:573:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c AppendXStringSets.c -o AppendXStringSets.o
AppendXStringSets.c: In function 'appendXStringSets':
AppendXStringSets.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'indexByContig':
ChainSegments.c:79:6: warning: unused variable 'n' [-Wunused-variable]
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:404:72: warning: 'upY' may be used uninitialized in this function [-Wuninitialized]
ChainSegments.c:452:8: warning: 'upX' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML':
ClusterML.c:400:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:214:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:195:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:128:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:124:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:444:14: warning: 'length' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:385:15: note: 'length' was declared here
ConsensusSequence.c:443:18: warning: 'lastPos' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:385:23: note: 'lastPos' was declared here
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1895:6: warning: 'd' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2020:6: warning: 'd' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c:58:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: 'lastCycle' was declared here
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: 'thisCycle' was declared here
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:239:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -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]
EnumerateSequence.c: In function 'enumerateGappedSequenceAA':
EnumerateSequence.c:364:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:160:9: warning: unused variable 'soFar' [-Wunused-variable]
FindFrameshifts.c:135:27: warning: 'K' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:381:14: warning: 'k' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:135:24: warning: 'J' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:135:21: warning: 'I' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.o
InsertGaps.c: In function 'insertGaps':
InsertGaps.c:47:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
MeltPolymer.c:36:6: warning: 'rans' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatch':
MultiMatch.c:184:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'firstMatchUpper':
MultiMatch.c:215:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchLists':
MultiMatch.c:244:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchListsDual':
MultiMatch.c:352:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrder':
MultiMatch.c:453:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrderDual':
MultiMatch.c:570:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
NNLS.c: In function 'NNLS':
NNLS.c:49:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Order.c -o Order.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.o
RemoveGaps.c: In function 'removeCommonGaps':
RemoveGaps.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c SubsetXStringSet.c -o SubsetXStringSet.o
SubsetXStringSet.c: In function 'subsetXStringSet':
SubsetXStringSet.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function 'terminalMismatch':
TerminalMismatch.c:40:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c Translate.c -o Translate.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -shared -s -static-libgcc -o DECIPHER.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:63:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
AlignProfiles.c: In function 'alignProfilesAA':
AlignProfiles.c:573:6: warning: variable 'NTHREADS' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c AppendXStringSets.c -o AppendXStringSets.o
AppendXStringSets.c: In function 'appendXStringSets':
AppendXStringSets.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'indexByContig':
ChainSegments.c:79:6: warning: unused variable 'n' [-Wunused-variable]
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:404:72: warning: 'upY' may be used uninitialized in this function [-Wuninitialized]
ChainSegments.c:452:8: warning: 'upX' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML':
ClusterML.c:400:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:214:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:281:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: 'minC' was declared here
ClusterNJ.c:280:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: 'minR' was declared here
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:128:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:200:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: 'minC' was declared here
ClusterUPGMA.c:199:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: 'minR' was declared here
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:444:14: warning: 'length' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:385:15: note: 'length' was declared here
ConsensusSequence.c:443:18: warning: 'lastPos' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c:385:23: note: 'lastPos' was declared here
ConsensusSequence.c:1725:6: warning: 'HEC' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1895:6: warning: 'd' may be used uninitialized in this function [-Wuninitialized]
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2020:6: warning: 'd' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c:58:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:37: note: 'lastCycle' was declared here
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wuninitialized]
DesignProbes.c:267:48: note: 'thisCycle' was declared here
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:239:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -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]
EnumerateSequence.c: In function 'enumerateGappedSequenceAA':
EnumerateSequence.c:364:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:160:9: warning: unused variable 'soFar' [-Wunused-variable]
FindFrameshifts.c:319:8: warning: 'K' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:381:14: warning: 'k' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:317:22: warning: 'J' may be used uninitialized in this function [-Wuninitialized]
FindFrameshifts.c:317:13: warning: 'I' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.o
InsertGaps.c: In function 'insertGaps':
InsertGaps.c:47:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
MeltPolymer.c:36:6: warning: 'rans' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatch':
MultiMatch.c:184:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'firstMatchUpper':
MultiMatch.c:215:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchLists':
MultiMatch.c:244:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchListsDual':
MultiMatch.c:352:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrder':
MultiMatch.c:453:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
MultiMatch.c: In function 'matchOrderDual':
MultiMatch.c:570:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
NNLS.c: In function 'NNLS':
NNLS.c:49:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Order.c -o Order.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.o
RemoveGaps.c: In function 'removeCommonGaps':
RemoveGaps.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c SubsetXStringSet.c -o SubsetXStringSet.o
SubsetXStringSet.c: In function 'subsetXStringSet':
SubsetXStringSet.c:44:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function 'terminalMismatch':
TerminalMismatch.c:40:6: warning: variable 'nthreads' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c Translate.c -o Translate.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"C:/biocbld/bbs-3.2-bioc/R/library/Biostrings/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/RSQLite/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/S4Vectors/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/IRanges/include" -I"C:/biocbld/bbs-3.2-bioc/R/library/XVector/include" -I"d:/RCompile/r-compiling/local/local320/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -shared -s -static-libgcc -o DECIPHER.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.16.0.zip
* DONE (DECIPHER)