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Package 129/514HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.0.0
Erik Wright
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/DECIPHER
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: DECIPHER
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DECIPHER_1.0.0.tar.gz
StartedAt: 2012-03-24 00:35:18 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:37:28 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 129.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/DECIPHER.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.0.0'
* 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 whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
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 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 examples ... OK
* 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

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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263: warning: ignoring #pragma omp parallel
ClusterNJ.c:273: warning: ignoring #pragma omp critical
ClusterNJ.c:433: warning: ignoring #pragma omp parallel
ClusterNJ.c:445: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:590: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:195: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:194: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:193: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:506: 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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:190: warning: ignoring #pragma omp critical
ClusterUPGMA.c:340: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:352: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:124: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:123: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:122: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:121: 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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171: warning: ignoring #pragma omp parallel
DistanceMatrix.c:133: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:133: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:131: 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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ReplaceChars.c -o ReplaceChars.o
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 ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DECIPHERing.Rnw' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded

* DONE (DECIPHER)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.9360.0571.014
BrowseDB0.0760.0280.138
BrowseSequences0.1440.0390.241
ConsensusSequence0.0290.0080.046
CreateChimeras2.0050.0362.067
DB2FASTA0.2780.0370.355
DistanceMatrix0.0140.0040.018
FindChimeras0.8050.0270.856
FormGroups0.0720.0050.077
IdClusters0.0540.0030.057
IdConsensus2.6130.1232.825
IdLengths0.0610.0170.085
IdentifyByRank0.0470.0050.053
SearchDB0.0440.0040.049
Seqs2DB0.7670.0850.860
TerminalChar0.0510.0120.074