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Package 166/658HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.5.1
Erik Wright
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DECIPHER
Last Changed Rev: 74767 / Revision: 74774
Last Changed Date: 2013-03-24 11:50:20 -0700 (Sun, 24 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DECIPHER
Version: 1.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DECIPHER_1.5.1.tar.gz
StartedAt: 2013-03-25 02:01:53 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:05:55 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 242.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.5.1'
* 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 ... OK
* checking package 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 for unstated 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
DB2FASTA: warning in writeXStringSet(myDNAStringSet, file = file,
  append = append): partial argument match of 'file' to 'filepath'
CreateChimeras: no visible binding for global variable 's1'
CreateChimeras: no visible binding for global variable 'd'
CreateChimeras: no visible binding for global variable 'myName'
* 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 for portable compilation flags in Makevars ... 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 examples ... [104s/105s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
TileSeqs 55.41 33.933  90.196
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package 'DECIPHER' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateDeltaG':
CalculateDeltaG.c:26: warning: 's2' may be used uninitialized in this function
CalculateDeltaG.c:26: warning: 's1' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c ClusterML.c -o ClusterML.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:266: warning: ignoring #pragma omp parallel
ClusterNJ.c:276: warning: ignoring #pragma omp critical
ClusterNJ.c:436: warning: ignoring #pragma omp parallel
ClusterNJ.c:448: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:593: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:198: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:198: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:197: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:196: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:509: warning: 'longestLeaf' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:183: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:193: warning: ignoring #pragma omp critical
ClusterUPGMA.c:343: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:355: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:127: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:127: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:126: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:125: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minR' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c CommonGaps.c -o CommonGaps.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c ConsensusSequence.c -o ConsensusSequence.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:174: warning: ignoring #pragma omp parallel
DistanceMatrix.c:136: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:136: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:134: warning: 'rPercentComplete' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatch':
MultiMatch.c:189: warning: ignoring #pragma omp parallel
MultiMatch.c: In function 'firstMatchUpper':
MultiMatch.c:215: warning: ignoring #pragma omp parallel
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_decipher.c -o R_init_decipher.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c ReplaceChars.c -o ReplaceChars.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic  -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function 'terminalMismatch':
TerminalMismatch.c:46: warning: ignoring #pragma omp parallel
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DECIPHERing.Rnw' 
   'DesignPrimers.Rnw' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded
* DONE (DECIPHER)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.9530.0721.027
BrowseDB0.0950.0390.135
BrowseSequences0.1910.0520.245
CalculateEfficiencyArray0.5040.0300.535
CalculateEfficiencyPCR0.0380.0070.045
ConsensusSequence0.0270.0070.034
CreateChimeras1.9970.1172.116
DB2FASTA0.0320.0370.069
DesignPrimers0.0090.0090.020
DistanceMatrix0.0250.0170.041
FindChimeras0.6670.0370.704
FormGroups0.0890.0120.101
IdClusters0.0720.0180.090
IdConsensus2.4020.1142.520
IdLengths0.0720.0260.098
IdentifyByRank0.0570.0120.068
SearchDB0.0600.0130.074
Seqs2DB0.8140.0920.908
TerminalChar0.0620.0190.081
TileSeqs55.41033.93390.196
deltaGrules0.1790.0230.203