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Package 41/260HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.8.18
H. Pages
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/Biostrings
Last Changed Rev: 33137 / Revision: 34573
Last Changed Date: 2008-08-08 10:48:41 -0700 (Fri, 08 Aug 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686 [ OK ] OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: Biostrings
Version: 2.8.18
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD build Biostrings
StartedAt: 2008-10-16 03:04:00 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 03:05:21 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 81.0 seconds
RetCode: 0
Status: OK
PackageFile: Biostrings_2.8.18.tar.gz
PackageFileSize: 570.9 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 *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ACtree_utils.c -o ACtree_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -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: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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
align_pairwiseAlignment.c: In function 'align_pairwiseAlignment':
align_pairwiseAlignment.c:125: warning: 'lookupValue' may be used uninitialized in this function
align_pairwiseAlignment.c:125: note: 'lookupValue' was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c bufutils.c -o bufutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c char_translate.c -o char_translate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c copy_seq.c -o copy_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:289: warning: label 'continue0' defined but not used
match_BOC2.c:235: warning: unused variable 'noffsets'
match_BOC2.c:235: warning: unused variable 'offsets'
match_BOC2.c:235: warning: unused variable 'j'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:332: warning: label 'continue0' defined but not used
match_BOC.c:269: warning: unused variable 'noffsets'
match_BOC.c:269: warning: unused variable 'offsets'
match_BOC.c:269: warning: unused variable 'j'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:371: warning: 'i2' may be used uninitialized in this function
match_pattern_boyermoore.c:371: warning: 'j1' may be used uninitialized in this function
match_pattern_boyermoore.c:371: warning: 'i1' may be used uninitialized in this function
match_pattern_boyermoore.c:372: warning: 'c' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_TBdna.c -o match_TBdna.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c match_utils.c -o match_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c MIndex_utils.c -o MIndex_utils.o
MIndex_utils.c: In function 'extract_endIndex':
MIndex_utils.c:77: warning: unused variable 'poffsets_order'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c replace_locs.c -o replace_locs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XInteger.c -o XInteger.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Biostrings.so ACtree_utils.o align_needwunsQS.o align_pairwiseAlignment.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o inject_code.o IRanges_class.o IRanges_utils.o match_BOC2.o match_BOC.o match_pattern_boyermoore.o match_pattern.o match_pattern_shiftor.o match_PWM.o match_reporting.o match_TBdna.o match_utils.o MIndex_utils.o pmatchPattern.o replace_locs.o R_init_Biostrings.o seqs_to_seqs.o SparseList_utils.o utils.o XInteger.o XRaw_class.o XRaw_utils.o XString_class.o XStringSet_class.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package 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 "update" 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 "append" in "Biostrings"
Creating a new generic function for "ls" in "Biostrings"
Creating a new generic function for "as.list" in "Biostrings"
Creating a new generic function for "toString" in "Biostrings"
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 "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"
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "coverage" no definition for class: "MIndex"
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"
** help
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \examples
 >>> 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
  BOC_SubjectString-class           text    html    latex
  Biostrings-internals              text    html    latex
  DNAString-class                   text    html    latex   example
  GENETIC_CODE                      text    html    latex   example
  IRanges-class                     text    html    latex   example
  IRanges-utils                     text    html    latex   example
  IUPAC_CODE_MAP                    text    html    latex   example
  MaskCollection-class              text    html    latex   example
  MaskedXString-class               text    html    latex   example
  PDict-class                       text    html    latex   example
  RNAString-class                   text    html    latex   example
  XString-class                     text    html    latex   example
  XStringAlign-class                text    html    latex   example
  XStringPartialMatches-class       text    html    latex
  XStringSet-class                  text    html    latex   example
  XStringSet-io                     text    html    latex   example
  XStringViews-class                text    html    latex   example
  XStringViews-constructors         text    html    latex   example
  align-utils                       text    html    latex   example
  alphabetFrequency                 text    html    latex   example
  chartr                            text    html    latex   example
  findPalindromes                   text    html    latex   example
  gregexpr2                         text    html    latex   example
  injectHardMask                    text    html    latex   example
  letter                            text    html    latex   example
  maskMotif                         text    html    latex   example
  match-utils                       text    html    latex   example
  matchLRPatterns                   text    html    latex   example
  matchPDict-exact                  text    html    latex   example
  matchPDict-inexact                text    html    latex   example
  matchPWM                          text    html    latex   example
  matchPattern                      text    html    latex   example
  matchProbePair                    text    html    latex   example
  needwunsQS                        text    html    latex   example
  pairwiseAlignment                 text    html    latex   example
  pmatchPattern                     text    html    latex   example
  read.Mask                         text    html    latex   example
  readFASTA                         text    html    latex   example
  replaceLetterAtLoc                text    html    latex   example
  reverse                           text    html    latex   example
  subXString                        text    html    latex   example
  substitution_matrices             text    html    latex   example
  toComplex                         text    html    latex
  yeastSEQCHR1                      text    html    latex   example
** building package indices ...
* 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_2.8.18.tar.gz'