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BioC 3.0: CHECK report for DECIPHER on zin1

This page was generated on 2015-04-10 09:39:34 -0700 (Fri, 10 Apr 2015).

Package 226/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 1.12.0
Erik Wright
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DECIPHER
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 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 

Summary

Package: DECIPHER
Version: 1.12.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.12.0.tar.gz
StartedAt: 2015-04-09 23:11:11 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:14:07 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 175.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/DECIPHER.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.12.0’
* 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 ... [15s/15s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    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
Add2DB: no visible global function definition for ‘dbDriver’
AlignDB: no visible global function definition for ‘dbDriver’
AlignSeqs: no visible binding for global variable ‘BLOSUM80’
AlignSeqs: no visible binding for global variable ‘BLOSUM62’
AlignSeqs: no visible binding for global variable ‘BLOSUM45’
BrowseDB: no visible global function definition for ‘dbDriver’
BrowseDB: no visible global function definition for ‘fetch’
DB2Seqs: no visible global function definition for ‘dbDriver’
DB2Seqs: no visible global function definition for ‘fetch’
FindChimeras: no visible global function definition for ‘dbDriver’
FindChimeras: no visible global function definition for ‘fetch’
FormGroups: no visible global function definition for ‘dbDriver’
FormGroups: no visible global function definition for ‘fetch’
IdConsensus: no visible global function definition for ‘dbDriver’
IdConsensus: no visible global function definition for ‘fetch’
IdLengths: no visible global function definition for ‘dbDriver’
IdentifyByRank: no visible global function definition for ‘dbDriver’
IdentifyByRank: no visible global function definition for ‘fetch’
SearchDB: no visible global function definition for ‘dbDriver’
SearchDB: no visible global function definition for ‘fetch’
Seqs2DB: no visible global function definition for ‘dbDriver’
TileSeqs: no visible global function definition for ‘dbDriver’
TileSeqs: no visible global function definition for ‘fetch’
* 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 ... [58s/46s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
TileSeqs        10.629  0.032  10.746
Array2Matrix    10.325  0.080   5.662
DesignArray     10.249  0.052   4.811
BrowseSequences  6.072  0.088   6.176
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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]
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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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 [-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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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:199:12: warning: ‘minC’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
ClusterUPGMA.c:198:12: warning: ‘minR’ may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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]
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: 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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c EnumerateSequence.c -o EnumerateSequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c GC_Content.c -o GC_Content.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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]
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 -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘matchOrder._omp_fn.1’:
MultiMatch.c:513:30: warning: ‘pos_x’ may be used uninitialized in this function [-Wuninitialized]
MultiMatch.c:471:8: note: ‘pos_x’ was declared here
MultiMatch.c:513:15: warning: ‘pos_y’ may be used uninitialized in this function [-Wuninitialized]
MultiMatch.c:471:15: note: ‘pos_y’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RSQLite/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o EnumerateSequence.o GC_Content.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.3000.0200.323
AlignDB2.4880.1082.603
AlignProfiles1.2040.0481.262
AlignSeqs2.8360.0682.092
AlignTranslation2.2640.0601.819
Amplify0.0000.0040.007
Array2Matrix10.325 0.080 5.662
BrowseDB0.0200.0120.033
BrowseSequences6.0720.0886.176
CalculateEfficiencyArray0.020.000.02
CalculateEfficiencyFISH0.0160.0040.018
CalculateEfficiencyPCR0.0160.0000.013
ConsensusSequence0.0080.0040.013
CreateChimeras1.8520.0361.453
DB2Seqs0.0120.0160.032
DesignArray10.249 0.052 4.811
DesignPrimers0.0040.0000.003
DesignProbes0.0040.0000.003
DistanceMatrix0.0800.0320.075
FindChimeras0.4560.0400.498
FormGroups0.1960.0000.196
IdClusters0.6040.0080.300
IdConsensus1.2760.0201.303
IdLengths0.0280.0040.034
IdentifyByRank0.0320.0000.034
MODELS000
MaskAlignment0.7520.0600.820
MeltDNA0.0360.0040.041
NNLS0.2000.0040.150
RESTRICTION_ENZYMES0.0080.0000.003
SearchDB0.0440.0200.062
Seqs2DB0.2840.0120.299
TerminalChar0.0240.0000.024
TileSeqs10.629 0.03210.746
deltaGrules0.0120.0040.013