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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 89/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
GeneticsBase0.99.0Gregory WarnesLast Changed Date: 2007-07-31 09:59:15 -0700 Last Changed Rev: 26068 | lamb1 | Linux (SUSE 10.1) | x86_64 | ERROR | skipped | |
wellington | Linux (SUSE 9.2) | i686 | ERROR | skipped | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | ERROR | skipped | skipped | |
pitt | Mac OS X (10.4.10) | i386 | [ ERROR ] | skipped | skipped |
Package: GeneticsBase |
Version: 0.99.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build GeneticsBase |
RetCode: 1 |
Time: 21.1 seconds |
Status: ERROR |
PackageFile: None |
* checking for file 'GeneticsBase/DESCRIPTION' ... OK * preparing 'GeneticsBase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * Installing *source* package 'GeneticsBase' ... ** libs ** arch - i386 g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -Wall -march=nocona -c LdMax.cpp -o LdMax.o g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -Wall -march=nocona -c convert.cpp -o convert.o g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -Wall -march=nocona -c getLDdist.cpp -o getLDdist.o g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -Wall -march=nocona -c readGenes.ped.cpp -o readGenes.ped.o readGenes.ped.cpp: In function 'int countLines(FILE*, int, int)': readGenes.ped.cpp:86: warning: 'tmpnc2' may be used uninitialized in this function g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -Wall -march=nocona -c register.cpp -o register.o g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o convert.o getLDdist.o readGenes.ped.o register.o -F/Library/Frameworks/R.framework/.. -framework R ** arch - ppc g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c LdMax.cpp -o LdMax.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c convert.cpp -o convert.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o readGenes.ped.cpp: In function 'int countLines(FILE*, int, int)': readGenes.ped.cpp:86: warning: 'tmpnc2' may be used uninitialized in this function g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c register.cpp -o register.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o convert.o getLDdist.o readGenes.ped.o register.o -F/Library/Frameworks/R.framework/.. -framework R ** R ** data ** inst WARNING: true value of 'SaveImage' is deprecated in favour of 'LazyLoad: true' ** save image Loading required package: combinat Attaching package: 'combinat' The following object(s) are masked from package:utils : combn Loading required package: xtable Loading required package: mvtnorm ** help Note: unmatched right brace in 'makeMarkerInfo' on or after line 7 >>> Building/Updating help pages for package 'GeneticsBase' Formats: text html latex example ALZH text html latex example Armitage text html latex example CAMP text html latex example HWE text html latex example HWE.chisq text html latex example HWE.exact text html latex example LD-class text html latex example LD text html latex example LDband-class text html latex example LDdist-class text html latex PGtables text html latex example PerlgenExample text html latex example PfizerExample text html latex example alleleCount text html latex example alleleLevels text html latex example alleleSummary text html latex example alleles text html latex example binsearch text html latex example callCodes text html latex example ci.balance text html latex example convert text html latex example decodeCallCodes text html latex example desMarkers text html latex example description text html latex example diseq text html latex example errorMetrics text html latex example extractAlleles text html latex example fastGrid text html latex example founderGeneSet text html latex example geneSet-class text html latex example geneSet2Ped text html latex example genotypeCoding text html latex example genotypeLevels text html latex example genotypeSummary text html latex example genotypes text html latex example gregorius text html latex example haplo.em.w text html latex example haplo.scan.w text html latex example haplo.score.slide.w text html latex example haplo.score.w text html latex example hapmapchr text html latex example homozygote text html latex example html text html latex example left text html latex example makeMarkerInfo text html latex example makeTransTable text html latex example makeTransTableList text html latex example markerInfo text html latex example markerNames text html latex example markerSummary text html latex example missingCodes text html latex example nallele text html latex example nmarker text html latex example notes text html latex example ped2geneSet text html latex phase text html latex example ploidy text html latex example print.LD text html latex example qtlex text html latex example read.pfizer text html latex example read.phe text html latex example readGenes text html latex example readGenes.ped text html latex example readGenes.perlegen text html latex example readGenes.pfizer text html latex example sampleInfo text html latex example studyInfo text html latex example transTables text html latex example xbat text html latex example ** building package indices ... Loading required package: methods Loading required package: combinat Attaching package: 'combinat' The following object(s) are masked from package:utils : combn Loading required package: xtable Loading required package: mvtnorm * DONE (GeneticsBase) * creating vignettes ... ERROR Loading required package: combinat Attaching package: 'combinat' The following object(s) are masked from package:utils : combn Loading required package: xtable Loading required package: mvtnorm Error: processing vignette 'SummaryTables.Rnw' failed with diagnostics: chunk 23 Error in write.GeneticsBaseSummary(x = x, filename = filename, ..., format = "latex") : could not find function "print.xtable" In addition: Warning messages: 1: In function (object) : geneSet Object has 2011 observations. Only first and last 6 displayed 2: In plot.window(...) : "labRow" is not a graphical parameter 3: In plot.xy(xy, type, ...) : "labRow" is not a graphical parameter 4: In title(...) : "labRow" is not a graphical parameter 5: In plot.window(...) : "labRow" is not a graphical parameter 6: In plot.xy(xy, type, ...) : "labRow" is not a graphical parameter 7: In title(...) : "labRow" is not a graphical parameter 8: In plot.window(...) : "labRow" is not a graphical parameter 9: In plot.xy(xy, type, ...) : "labRow" is not a graphical parameter 10: In title(...) : "labRow" is not a graphical parameter Execution halted