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:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DECIPHER_1.16.0.tar.gz
###
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* 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 8.3Mb
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 ... [179s/179s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
CorrectFrameshifts 37.032 2.047 39.083
StaggerAlignment 33.216 0.169 33.455
AlignTranslation 21.327 0.139 21.470
AlignSeqs 16.468 0.077 16.546
TileSeqs 11.937 0.007 11.945
BrowseSeqs 10.079 0.070 10.164
Array2Matrix 8.750 0.042 8.792
DesignArray 8.273 0.047 8.318
AlignSynteny 5.341 0.282 6.128
* 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.
* 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)