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Package 42/264HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.7.44
H. Pages
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
Last Changed Rev: 30943 / Revision: 30951
Last Changed Date: 2008-04-08 20:04:16 -0700 (Tue, 08 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ OK ] WARNINGS  OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: Biostrings
Version: 2.7.44
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build Biostrings
StartedAt: 2008-04-09 03:13:26 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 03:15:00 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 93.2 seconds
RetCode: 0
Status: OK
PackageFile: Biostrings_2.7.44.tar.gz
PackageFileSize: 596.7 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-2.2-bioc/tmpdir/Rinst170477258


---------- Making package Biostrings ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making ACtree_utils.d from ACtree_utils.c
making IRanges_class.d from IRanges_class.c
making IRanges_utils.d from IRanges_utils.c
making MIndex_utils.d from MIndex_utils.c
making R_init_Biostrings.d from R_init_Biostrings.c
making XInteger.d from XInteger.c
making XRaw_class.d from XRaw_class.c
making XRaw_utils.d from XRaw_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 bufutils.d from bufutils.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 find_palindromes.d from find_palindromes.c
making match_BOC.d from match_BOC.c
making match_BOC2.d from match_BOC2.c
making match_TBdna.d from match_TBdna.c
making match_boyermoore.d from match_boyermoore.c
making match_naive.d from match_naive.c
making match_shiftor.d from match_shiftor.c
making normalize_views.d from normalize_views.c
making pmatchPattern.d from pmatchPattern.c
making replace_locs.d from replace_locs.c
making seqs_to_seqs.d from seqs_to_seqs.c
making utils.d from utils.c
making views_buffer.d from views_buffer.c
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c ACtree_utils.c -o ACtree_utils.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c IRanges_class.c -o IRanges_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function 'reduce_IRanges':
IRanges_utils.c:191: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'extract_endIndex':
MIndex_utils.c:95: warning: unused variable 'poffsets_order'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XInteger.c -o XInteger.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XRaw_class.c -o XRaw_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XRaw_utils.c -o XRaw_utils.o
XRaw_utils.c: In function 'XRaw_loadFASTA':
XRaw_utils.c:552: warning: 'view_start' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XStringSet_class.c -o XStringSet_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c XString_class.c -o XString_class.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:38: warning: 'lkup_val' may be used uninitialized in this function
align_needwunsQS.c:38: note: 'lkup_val' was declared here
align_needwunsQS.c:25: warning: 'sc' may be used uninitialized in this function
align_needwunsQS.c:25: note: 'sc' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c bufutils.c -o bufutils.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c char_frequency.c -o char_frequency.o
char_frequency.c: In function 'oligonucleotide_frequency':
char_frequency.c:159: warning: 'ans_offset' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c char_translate.c -o char_translate.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c copy_seq.c -o copy_seq.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/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-2.2-bioc/R/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'
match_BOC.c: In function 'match_BOC_preprocess':
match_BOC.c:29: warning: 'pre4' may be used uninitialized in this function
match_BOC.c:29: note: 'pre4' was declared here
match_BOC.c: In function 'match_BOC_exact':
match_BOC.c:38: warning: 'pre4' is used uninitialized in this function
match_BOC.c:29: note: 'pre4' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/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'
match_BOC2.c: In function 'match_BOC2_exact':
match_BOC2.c:54: warning: 'pre4' is used uninitialized in this function
match_BOC2.c:45: note: 'pre4' was declared here
match_BOC2.c: In function 'match_BOC2_preprocess':
match_BOC2.c:45: warning: 'pre4' may be used uninitialized in this function
match_BOC2.c:45: note: 'pre4' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_TBdna.c -o match_TBdna.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_boyermoore.c -o match_boyermoore.o
match_boyermoore.c: In function 'match_boyermoore':
match_boyermoore.c:372: warning: 'c' may be used uninitialized in this function
match_boyermoore.c:372: note: 'c' was declared here
match_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function
match_boyermoore.c:371: note: 'j1' was declared here
match_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function
match_boyermoore.c:371: note: 'i2' was declared here
match_boyermoore.c:371: warning: 'i1' may be used uninitialized in this function
match_boyermoore.c:371: note: 'i1' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_naive.c -o match_naive.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c match_shiftor.c -o match_shiftor.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c normalize_views.c -o normalize_views.o
normalize_views.c:49: warning: 'normalize_orderedbystartviews' defined but not used
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c pmatchPattern.c -o pmatchPattern.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c replace_locs.c -o replace_locs.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c seqs_to_seqs.c -o seqs_to_seqs.o
seqs_to_seqs.c: In function 'copy_subXRaw':
seqs_to_seqs.c:191: warning: unused variable 'ans'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c utils.c -o utils.o
utils.c: In function '_Biostrings_coerce_to_complex_from_i1i2':
utils.c:492: warning: 'lkup_val.r' may be used uninitialized in this function
utils.c:492: warning: 'lkup_val.i' may be used uninitialized in this function
utils.c: In function '_Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:448: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_subset':
utils.c:367: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_to_i1i2':
utils.c:326: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_subset':
utils.c:286: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function '_Biostrings_translate_charcpy_from_i1i2':
utils.c:245: warning: 'lkup_val' may be used uninitialized in this function
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c views_buffer.c -o views_buffer.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i Biostrings_res.rc -o Biostrings_res.o
gcc  -std=gnu99  -shared -s  -o Biostrings.dll Biostrings.def ACtree_utils.o IRanges_class.o IRanges_utils.o MIndex_utils.o R_init_Biostrings.o XInteger.o XRaw_class.o XRaw_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o match_BOC.o match_BOC2.o match_TBdna.o match_boyermoore.o match_naive.o match_shiftor.o normalize_views.o pmatchPattern.o replace_locs.o seqs_to_seqs.o utils.o views_buffer.o Biostrings_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package Biostrings for lazy loading
Creating a new generic function for "start" in "Biostrings"
Creating a new generic function for "end" in "Biostrings"
Creating a new generic function for "as.data.frame" in "Biostrings"
Creating a new generic function for "duplicated" in "Biostrings"
Creating a new generic function for "as.matrix" in "Biostrings"
Creating a new generic function for "update" in "Biostrings"
Creating a new generic function for "toString" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XString" no definition for class: "AsIs"
Creating a new generic function for "nchar" 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"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "XStringSet" no definition for class: "AsIs"
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"
New generic for "chartr" does not agree with implicit generic from package "base"; a new generic will be assigned with package "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"
Creating a new generic function for "unlist" in "Biostrings"
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
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \description
Note: removing empty section \examples
 >>> 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
  Biostrings-internals              text    html    latex           chm
  DNAString-class                   text    html    latex   example chm
  GENETIC_CODE                      text    html    latex   example chm
  IRanges-class                     text    html    latex   example chm
  IRanges-utils                     text    html    latex   example chm
  IUPAC_CODE_MAP                    text    html    latex   example chm
  PDict-class                       text    html    latex   example chm
  RNAString-class                   text    html    latex   example chm
  XString-class                     text    html    latex   example chm
  XStringAlign-class                text    html    latex   example chm
  XStringPartialMatches-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
  findPalindromes                   text    html    latex   example chm
  gregexpr2                         text    html    latex   example chm
  letter                            text    html    latex   example chm
  mask                              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
  matchPattern                      text    html    latex   example chm
  matchProbePair                    text    html    latex   example chm
  needwunsQS                        text    html    latex   example chm
  pmatchPattern                     text    html    latex   example chm
  readFASTA                         text    html    latex   example chm
  replaceLetterAtLoc                text    html    latex   example chm
  reverseComplement                 text    html    latex   example chm
  subXString                        text    html    latex   example chm
  substitution_matrices             text    html    latex   example chm
  toComplex                         text    html    latex           chm
  yeastSEQCHR1                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.2-bioc\meat\Biostrings\chm\Biostrings.chm





Compile time: 0 minutes, 1 second

39	Topics

843	Local links

1	Internet link

1	Graphic





Created e:\biocbld\bbs-2.2-bioc\meat\Biostrings\chm\Biostrings.chm, 101,361 bytes

Compression decreased file by 235,705 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_2.7.44.tar.gz'