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BioC 3.2: CHECK report for DECIPHER on perceval

This page was generated on 2015-11-10 14:47:14 -0800 (Tue, 10 Nov 2015).

Package 256/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 1.16.0
Erik Wright
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DECIPHER
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DECIPHER_1.16.0.tar.gz
StartedAt: 2015-11-10 04:03:28 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 04:09:01 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 333.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DECIPHER_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DECIPHER.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       3.7Mb
    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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [178s/178s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
CorrectFrameshifts 36.665  1.972  38.639
StaggerAlignment   32.880  0.135  33.017
AlignTranslation   21.489  0.118  21.609
AlignSeqs          16.446  0.086  16.532
TileSeqs           12.070  0.006  12.077
BrowseSeqs         10.053  0.071  10.135
Array2Matrix        8.671  0.040   8.713
DesignArray         8.183  0.044   8.228
AlignSynteny        5.362  0.281   5.672
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package ‘DECIPHER’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:265: warning: ignoring #pragma omp parallel
AlignProfiles.c: In function ‘alignProfilesAA’:
AlignProfiles.c:958: warning: ignoring #pragma omp parallel
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c AppendXStringSets.c -o AppendXStringSets.o
AppendXStringSets.c: In function ‘appendXStringSets’:
AppendXStringSets.c:82: warning: ignoring #pragma omp parallel
AppendXStringSets.c:88: warning: ignoring #pragma omp parallel
AppendXStringSets.c:44: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c AssignIndels.c -o AssignIndels.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c CalculateDeltaG.c -o CalculateDeltaG.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:26: warning: missing braces around initializer
CalculateFISH.c:26: warning: (near initialization for ‘dH_DR[0]’)
CalculateFISH.c:32: warning: missing braces around initializer
CalculateFISH.c:32: warning: (near initialization for ‘dS_DR[0]’)
CalculateFISH.c:38: warning: missing braces around initializer
CalculateFISH.c:38: warning: (near initialization for ‘dH_DD[0]’)
CalculateFISH.c:44: warning: missing braces around initializer
CalculateFISH.c:44: warning: (near initialization for ‘dS_DD[0]’)
CalculateFISH.c:50: warning: missing braces around initializer
CalculateFISH.c:50: warning: (near initialization for ‘dH_RR[0]’)
CalculateFISH.c:56: warning: missing braces around initializer
CalculateFISH.c:56: warning: (near initialization for ‘dS_RR[0]’)
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘indexByContig’:
ChainSegments.c:79: warning: unused variable ‘n’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML’:
ClusterML.c:422: warning: ignoring #pragma omp parallel
ClusterML.c:427: warning: ignoring #pragma omp parallel
ClusterML.c:432: warning: ignoring #pragma omp parallel
ClusterML.c:400: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ’:
ClusterNJ.c:267: warning: ignoring #pragma omp parallel
ClusterNJ.c:277: warning: ignoring #pragma omp critical
ClusterNJ.c:437: warning: ignoring #pragma omp parallel
ClusterNJ.c:449: warning: ignoring #pragma omp parallel
ClusterNJ.c:214: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA’:
ClusterUPGMA.c:186: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:196: warning: ignoring #pragma omp critical
ClusterUPGMA.c:376: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:388: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:128: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c CommonGaps.c -o CommonGaps.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Compositions.c -o Compositions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConsensusSequence.c -o ConsensusSequence.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConsolidateGaps.c -o ConsolidateGaps.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71: warning: missing braces around initializer
DesignProbes.c:71: warning: (near initialization for ‘NN[0]’)
DesignProbes.c:78: warning: missing braces around initializer
DesignProbes.c:78: warning: (near initialization for ‘PM[0]’)
DesignProbes.c:85: warning: missing braces around initializer
DesignProbes.c:85: warning: (near initialization for ‘sMM[0]’)
DesignProbes.c:256: warning: ignoring #pragma omp parallel
DesignProbes.c:707: warning: ignoring #pragma omp critical
DesignProbes.c:58: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘distMatrix’:
DistanceMatrix.c:293: warning: ignoring #pragma omp parallel
DistanceMatrix.c:239: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c EnumerateSequence.c -o EnumerateSequence.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:160: warning: unused variable ‘soFar’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c InsertGaps.c -o InsertGaps.o
InsertGaps.c: In function ‘insertGaps’:
InsertGaps.c:83: warning: ignoring #pragma omp parallel
InsertGaps.c:47: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IntDist.c -o IntDist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:80: warning: missing braces around initializer
MeltPolymer.c:80: warning: (near initialization for ‘dH[0]’)
MeltPolymer.c:89: warning: missing braces around initializer
MeltPolymer.c:89: warning: (near initialization for ‘dS[0]’)
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatch’:
MultiMatch.c:190: warning: ignoring #pragma omp parallel
MultiMatch.c:184: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘firstMatchUpper’:
MultiMatch.c:217: warning: ignoring #pragma omp parallel
MultiMatch.c:215: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchLists’:
MultiMatch.c:258: warning: ignoring #pragma omp parallel
MultiMatch.c:244: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchListsDual’:
MultiMatch.c:363: warning: ignoring #pragma omp parallel
MultiMatch.c:352: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchOrder’:
MultiMatch.c:467: warning: ignoring #pragma omp parallel
MultiMatch.c:453: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchOrderDual’:
MultiMatch.c:573: warning: ignoring #pragma omp parallel
MultiMatch.c:570: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c NNLS.c -o NNLS.o
NNLS.c: In function ‘NNLS’:
NNLS.c:89: warning: ignoring #pragma omp parallel
NNLS.c:49: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Order.c -o Order.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PredictHEC.c -o PredictHEC.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_decipher.c -o R_init_decipher.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RemoveGaps.c -o RemoveGaps.o
RemoveGaps.c: In function ‘removeCommonGaps’:
RemoveGaps.c:133: warning: ignoring #pragma omp parallel
RemoveGaps.c:44: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ReplaceChars.c -o ReplaceChars.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SubsetXStringSet.c -o SubsetXStringSet.o
SubsetXStringSet.c: In function ‘subsetXStringSet’:
SubsetXStringSet.c:76: warning: ignoring #pragma omp parallel
SubsetXStringSet.c:44: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function ‘terminalMismatch’:
TerminalMismatch.c:47: warning: ignoring #pragma omp parallel
TerminalMismatch.c:40: warning: unused variable ‘nthreads’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Translate.c -o Translate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.3840.0090.404
AdjustAlignment0.3500.0120.363
AlignDB2.7560.0592.815
AlignProfiles1.7510.0311.825
AlignSeqs16.446 0.08616.532
AlignSynteny5.3620.2815.672
AlignTranslation21.489 0.11821.609
AmplifyDNA0.0050.0010.031
Array2Matrix8.6710.0408.713
BrowseDB0.0270.0010.029
BrowseSeqs10.053 0.07110.135
CalculateEfficiencyArray0.0200.0070.026
CalculateEfficiencyFISH0.0110.0000.011
CalculateEfficiencyPCR0.0120.0000.011
ConsensusSequence0.0160.0000.016
CorrectFrameshifts36.665 1.97238.639
CreateChimeras1.2400.0071.249
DB2Seqs0.0190.0140.100
DesignArray8.1830.0448.228
DesignPrimers0.0010.0000.002
DesignProbes0.0010.0000.002
DesignSignatures0.0020.0010.002
DigestDNA0.2240.0130.237
Disambiguate0.0830.0010.084
DistanceMatrix0.0170.0120.031
FindChimeras0.0970.0020.099
FindSynteny2.6240.0082.632
FormGroups0.2280.0030.230
HEC_MI0.2840.0150.301
IdClusters0.0520.0080.062
IdConsensus1.4090.0331.443
IdLengths0.0320.0010.034
IdentifyByRank0.0310.0010.032
MIQS0.0070.0020.019
MODELS0.0010.0000.001
MaskAlignment0.8610.0090.870
MeltDNA0.0770.0030.086
NNLS0.0110.0080.017
OrientNucleotides1.0640.0241.089
PredictHEC0.4180.0110.428
RESTRICTION_ENZYMES0.0020.0010.003
SearchDB0.0620.0040.066
Seqs2DB0.3180.0030.320
StaggerAlignment32.880 0.13533.017
Synteny-class3.8290.0263.857
TerminalChar0.0310.0010.032
TileSeqs12.070 0.00612.077
deltaGrules0.0150.0090.024
deltaHrules0.0270.0070.034
deltaSrules0.0780.0060.084