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Package 47/294HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.10.22
H. Pages
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/Biostrings
Last Changed Rev: 38413 / Revision: 38965
Last Changed Date: 2009-04-02 10:19:41 -0700 (Thu, 02 Apr 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ OK ] WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  WARNINGS  OK 
Package: Biostrings
Version: 2.10.22
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD build Biostrings
StartedAt: 2009-04-18 15:59:07 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 16:03:08 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 240.3 seconds
RetCode: 0
Status: OK
PackageFile: Biostrings_2.10.22.tar.gz
PackageFileSize: 837.1 KiB

Command output

* checking for file 'Biostrings/DESCRIPTION' ... OK
* preparing 'Biostrings':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.3-bioc/tmpdir/Rinst537698190


---------- Making package Biostrings ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making Dups_utils.d from Dups_utils.c
making IRanges_stubs.d from IRanges_stubs.c
making MIndex_utils.d from MIndex_utils.c
making PreprocessedTB_class.d from PreprocessedTB_class.c
making R_init_Biostrings.d from R_init_Biostrings.c
making RoSeq_utils.d from RoSeq_utils.c
making SparseList_utils.d from SparseList_utils.c
making XStringSet_class.d from XStringSet_class.c
making XString_class.d from XString_class.c
making align_needwunsQS.d from align_needwunsQS.c
making align_pairwiseAlignment.d from align_pairwiseAlignment.c
making align_utils.d from align_utils.c
making char_frequency.d from char_frequency.c
making char_translate.d from char_translate.c
making copy_seq.d from copy_seq.c
making fasta_io.d from fasta_io.c
making find_palindromes.d from find_palindromes.c
making inject_code.d from inject_code.c
making match_BOC.d from match_BOC.c
making match_BOC2.d from match_BOC2.c
making match_PWM.d from match_PWM.c
making match_pattern.d from match_pattern.c
making match_pattern_at.d from match_pattern_at.c
making match_pattern_boyermoore.d from match_pattern_boyermoore.c
making match_pattern_indels.d from match_pattern_indels.c
making match_pattern_shiftor.d from match_pattern_shiftor.c
making match_pdict.d from match_pdict.c
making match_pdict_ACtree.d from match_pdict_ACtree.c
making match_pdict_ACtree2.d from match_pdict_ACtree2.c
making match_pdict_Twobit.d from match_pdict_Twobit.c
making match_reporting.d from match_reporting.c
making pmatchPattern.d from pmatchPattern.c
making replace_letter_at.d from replace_letter_at.c
making utils.d from utils.c
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c Dups_utils.c -o Dups_utils.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'ByName_MIndex_endIndex':
MIndex_utils.c:220: warning: unused variable 'poffsets_order'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c RoSeq_utils.c -o RoSeq_utils.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c SparseList_utils.c -o SparseList_utils.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c XStringSet_class.c -o XStringSet_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c XString_class.c -o XString_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:39: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:39: note: 'lkup_val' was declared here
align_needwunsQS.c:26: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:26: note: 'sc' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignedFixedSubject_align_aligned':
align_utils.c:222: warning: 'indelWidthSubject' may be used uninitialized in this function
align_utils.c:222: warning: 'indelStartSubject' may be used uninitialized in this function
align_utils.c:222: warning: 'indelWidthPattern' may be used uninitialized in this function
align_utils.c:222: warning: 'indelStartPattern' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c char_frequency.c -o char_frequency.o
char_frequency.c: In function 'oligonucleotide_frequency':
char_frequency.c:207: warning: 'ans_offset' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c char_translate.c -o char_translate.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c copy_seq.c -o copy_seq.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c fasta_io.c -o fasta_io.o
fasta_io.c:54: warning: 'add_desc_LENGTHONLY' defined but not used
fasta_io.c:89: warning: 'add_empty_seq_CHARAEAE' defined but not used
fasta_io.c:95: warning: 'append_to_last_seq_CHARAEAE' defined but not used
fasta_io.c:109: warning: 'add_desc1' defined but not used
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c find_palindromes.c -o find_palindromes.o
find_palindromes.c: In function 'find_palindromes':
find_palindromes.c:25: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:25: note: 'letter0' was declared here
find_palindromes.c:24: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:24: note: 'all_letter0' was declared here
find_palindromes.c:79: warning: 'letter0' may be used uninitialized in this function
find_palindromes.c:79: note: 'letter0' was declared here
find_palindromes.c:78: warning: 'lkup_val' may be used uninitialized in this function
find_palindromes.c:78: note: 'lkup_val' was declared here
find_palindromes.c:78: warning: 'all_letter0' may be used uninitialized in this function
find_palindromes.c:78: note: 'all_letter0' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c inject_code.c -o inject_code.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:331: warning: label 'continue0' defined but not used
match_BOC.c:268: warning: unused variable 'noffsets'
match_BOC.c:268: warning: unused variable 'offsets'
match_BOC.c:268: warning: unused variable 'j'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:288: warning: label 'continue0' defined but not used
match_BOC2.c:234: warning: unused variable 'noffsets'
match_BOC2.c:234: warning: unused variable 'offsets'
match_BOC2.c:234: warning: unused variable 'j'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_PWM.c -o match_PWM.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pattern.c -o match_pattern.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pattern_at.c -o match_pattern_at.o
match_pattern_at.c: In function '_nedit_for_Proffset':
match_pattern_at.c:292: warning: unused variable 'Pc'
match_pattern_at.c:291: warning: unused variable 'j'
match_pattern_at.c:291: warning: unused variable 'jmin'
match_pattern_at.c:291: warning: unused variable 'iplus1'
match_pattern_at.c:291: warning: unused variable 'i'
match_pattern_at.c:291: warning: unused variable 'b'
match_pattern_at.c:291: warning: unused variable 'B'
match_pattern_at.c:290: warning: unused variable 'row_length'
match_pattern_at.c:290: warning: unused variable 'curr_row'
match_pattern_at.c:290: warning: unused variable 'prev_row'
match_pattern_at.c:290: warning: unused variable 'max_nedit_plus1'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:374: warning: 'c' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:373: warning: 'i1' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pattern_indels.c -o match_pattern_indels.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'XStringSet_vmatch_pdict':
match_pdict.c:359: warning: 'ans' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pdict_ACtree.c -o match_pdict_ACtree.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function 'walk_subject':
match_pdict_Twobit.c:187: warning: 'twobit_sign' may be used uninitialized in this function
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:132: warning: 'twobit_sign2pos' may be used uninitialized in this function
match_pdict_Twobit.c: In function '_match_Twobit':
match_pdict_Twobit.c:187: warning: 'twobit_sign' may be used uninitialized in this function
match_pdict_Twobit.c:187: note: 'twobit_sign' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c match_reporting.c -o match_reporting.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c pmatchPattern.c -o pmatchPattern.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c replace_letter_at.c -o replace_letter_at.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/IRanges/include"    -O3 -Wall  -c utils.c -o utils.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include  -i Biostrings_res.rc -o Biostrings_res.o
gcc  -std=gnu99  -shared -s  -o Biostrings.dll Biostrings.def Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o char_frequency.o char_translate.o copy_seq.o fasta_io.o find_palindromes.o inject_code.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_at.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree.o match_pdict_ACtree2.o match_pdict_Twobit.o match_reporting.o pmatchPattern.o replace_letter_at.o utils.o Biostrings_res.o  -Le:/biocbld/bbs-2.3-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package Biostrings for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 rbind,
	 sapply 

Creating a new generic function for "nchar" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XString" no definition for class: "AsIs"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XStringSet" no definition for class: "AsIs"
Creating a generic for "order" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (...), (na.last, decreasing))
Creating a new generic function for "sort" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "BStringViews" no definition for class: "file"
Creating a generic for "substr" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "substring" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ (in default values?))
Creating a generic for "chartr" in package  "Biostrings"
    (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ:  (x), (old, new, x))
Creating a new generic function for "ls" in "Biostrings"
Creating a new generic function for "head" in "Biostrings"
Creating a new generic function for "tail" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "PDict" no definition for class: "AsIs"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "eq" no definition for class: "BioString"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'Biostrings'
     Formats: text html latex example chm 
  AAString-class                    text    html    latex   example chm
  AMINO_ACID_CODE                   text    html    latex   example chm
  AlignedXStringSet-class           text    html    latex   example chm
  BOC_SubjectString-class           text    html    latex           chm
  Biostrings-internals              text    html    latex           chm
  DNAString-class                   text    html    latex   example chm
  GENETIC_CODE                      text    html    latex   example chm
  IUPAC_CODE_MAP                    text    html    latex   example chm
Note: removing empty section \examples in file 'InDel-class.Rd'
Note: removing empty section \examples in file 'InDel-class.Rd'
  InDel-class                       text    html    latex           chm
  MIndex-class                      text    html    latex   example chm
  MaskedXString-class               text    html    latex   example chm
  PDict-class                       text    html    latex   example chm
  PairwiseAlignedFixedSubject-class text    html    latex   example chm
  QualityScaledXStringSet-class     text    html    latex   example chm
  RNAString-class                   text    html    latex   example chm
  XString-class                     text    html    latex   example chm
  XStringPartialMatches-class       text    html    latex           chm
  XStringQuality-class              text    html    latex   example chm
  XStringSet-class                  text    html    latex   example chm
  XStringSet-io                     text    html    latex   example chm
  XStringViews-class                text    html    latex   example chm
  XStringViews-constructors         text    html    latex   example chm
  align-utils                       text    html    latex   example chm
  alphabetFrequency                 text    html    latex   example chm
  chartr                            text    html    latex   example chm
  findPalindromes                   text    html    latex   example chm
  gregexpr2                         text    html    latex   example chm
  injectHardMask                    text    html    latex   example chm
  letter                            text    html    latex   example chm
  maskMotif                         text    html    latex   example chm
  match-utils                       text    html    latex   example chm
  matchLRPatterns                   text    html    latex   example chm
  matchPDict-exact                  text    html    latex   example chm
  matchPDict-inexact                text    html    latex   example chm
  matchPWM                          text    html    latex   example chm
  matchPattern                      text    html    latex   example chm
  matchProbePair                    text    html    latex   example chm
  needwunsQS                        text    html    latex   example chm
  pairwiseAlignment                 text    html    latex   example chm
  phiX174Phage                      text    html    latex   example chm
  pid                               text    html    latex   example chm
  pmatchPattern                     text    html    latex           chm
  readFASTA                         text    html    latex   example chm
  replaceLetterAt                   text    html    latex   example chm
  reverse                           text    html    latex   example chm
  stringDist                        text    html    latex   example chm
  subXString                        text    html    latex           chm
  substitution_matrices             text    html    latex   example chm
  toComplex                         text    html    latex   example chm
  translate                         text    html    latex   example chm
  yeastSEQCHR1                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.3-bioc\meat\Biostrings\chm\Biostrings.chm





Compile time: 0 minutes, 4 seconds

52	Topics

1,313	Local links

4	Internet links

1	Graphic





Created e:\biocbld\bbs-2.3-bioc\meat\Biostrings\chm\Biostrings.chm, 153,655 bytes

Compression decreased file by 395,330 bytes.

  adding MD5 sums

* DONE (Biostrings)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Biostrings_2.10.22.tar.gz'