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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 39/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
Biostrings2.5.19H. PagesLast Changed Date: 2007-08-13 12:36:50 -0700 Last Changed Rev: 26368 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | OK | [ OK ] |
Package: Biostrings |
Version: 2.5.19 |
Command: /Users/biocbuild/BBS/utils/build-universal.sh Biostrings_2.5.19.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biostrings.buildbin-libdir |
RetCode: 0 |
Time: 13.5 seconds |
Status: OK |
PackageFile: Biostrings_2.5.19.tgz |
INSTALLATION WITH 'R CMD INSTALL Biostrings_2.5.19.tar.gz' * Installing to library 'Biostrings.buildbin-libdir' * Installing *source* package 'Biostrings' ... ** libs ** arch - i386 gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c R_init_Biostrings.c -o R_init_Biostrings.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c XInteger.c -o XInteger.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c XRaw.c -o XRaw.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c align_needwunsQS.c -o align_needwunsQS.o align_needwunsQS.c: In function 'align_needwunsQS': align_needwunsQS.c:25: warning: 'sc' may be used uninitialized in this function align_needwunsQS.c:38: warning: 'lkup_val' may be used uninitialized in this function gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c char_frequency.c -o char_frequency.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c match_boyermoore.c -o match_boyermoore.o match_boyermoore.c: In function 'match_boyermoore': match_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function match_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function match_boyermoore.c:371: warning: 'i1' may be used uninitialized in this function gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c match_naive.c -o match_naive.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c match_shiftor.c -o match_shiftor.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c normalize_views.c -o normalize_views.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c pmatchPattern.c -o pmatchPattern.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c reverseComplement.c -o reverseComplement.o gcc-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 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c utils.c -o utils.o utils.c: In function '_Biostrings_translate_charcpy_from_i1i2': utils.c:240: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_from_subset': utils.c:279: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_to_i1i2': utils.c:319: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_to_subset': utils.c:358: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_reverse_translate_charcpy_from_i1i2': utils.c:437: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_coerce_to_complex_from_i1i2': utils.c:479: warning: 'lkup_val.r' may be used uninitialized in this function utils.c:479: warning: 'lkup_val.i' may be used uninitialized in this function gcc-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 Biostrings.so R_init_Biostrings.o XInteger.o XRaw.o align_needwunsQS.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o normalize_views.o pmatchPattern.o reverseComplement.o utils.o -F/Library/Frameworks/R.framework/.. -framework R ** arch - ppc gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 R_init_Biostrings.c -o R_init_Biostrings.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 XInteger.c -o XInteger.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 XRaw.c -o XRaw.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 align_needwunsQS.c -o align_needwunsQS.o align_needwunsQS.c: In function 'align_needwunsQS': align_needwunsQS.c:25: warning: 'sc' may be used uninitialized in this function align_needwunsQS.c:38: warning: 'lkup_val' may be used uninitialized in this function gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 char_frequency.c -o char_frequency.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 match_boyermoore.c -o match_boyermoore.o match_boyermoore.c: In function 'match_boyermoore': match_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function match_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function match_boyermoore.c:371: warning: 'i1' may be used uninitialized in this function gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 match_naive.c -o match_naive.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 match_shiftor.c -o match_shiftor.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 normalize_views.c -o normalize_views.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 pmatchPattern.c -o pmatchPattern.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 reverseComplement.c -o reverseComplement.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -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 utils.c -o utils.o utils.c: In function '_Biostrings_translate_charcpy_from_i1i2': utils.c:240: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_from_subset': utils.c:279: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_to_i1i2': utils.c:319: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_translate_charcpy_to_subset': utils.c:358: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_reverse_translate_charcpy_from_i1i2': utils.c:437: warning: 'lkup_val' may be used uninitialized in this function utils.c: In function '_Biostrings_coerce_to_complex_from_i1i2': utils.c:479: warning: 'lkup_val.r' may be used uninitialized in this function utils.c:479: warning: 'lkup_val.i' may be used uninitialized in this function gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so R_init_Biostrings.o XInteger.o XRaw.o align_needwunsQS.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o normalize_views.o pmatchPattern.o reverseComplement.o utils.o -F/Library/Frameworks/R.framework/.. -framework R ** R ** data ** inst ** preparing package for lazy loading Creating a new generic function for "toString" in "Biostrings" Creating a new generic function for "nchar" in "Biostrings" Creating a new generic function for "as.matrix" in "Biostrings" Creating a new generic function for "as.list" in "Biostrings" Warning in matchSignature(signature, fdef, where) : in the method signature for function "BStringViews" no definition for class: "file" New generic for "substr" does not agree with implicit generic from package "base"; a new generic will be assigned with package "Biostrings" New generic for "substring" does not agree with implicit generic from package "base"; a new generic will be assigned with package "Biostrings" Warning in matchSignature(signature, fdef, where) : in the method signature for function "eq" no definition for class: "BioString" ** help >>> Building/Updating help pages for package 'Biostrings' Formats: text html latex example AAString-class text html latex example AMINO_ACID_CODE text html latex example BString-class text html latex example BStringAlign-class text html latex example BStringPartialMatches-class text html latex example BStringViews-class text html latex example BStringViews-constructors text html latex example BStringViews-io text html latex example Biostrings-internals text html latex DNAString-class text html latex example GENETIC_CODE text html latex example IUPAC_CODE_MAP text html latex example RNAString-class text html latex example alphabetFrequency text html latex example gregexpr2 text html latex example letter text html latex example mask text html latex example matchPattern text html latex example matchProbePair text html latex example needwunsQS text html latex example pmatchPattern text html latex example readFASTA text html latex example reverseComplement text html latex example scoring_matrices text html latex example subBString text html latex example toComplex text html latex example yeastSEQCHR1 text html latex example ** building package indices ... * DONE (Biostrings)