biocLite (BioC 2.0): BUILD report for Biostrings on liverpool

* 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-2.0-biocLite/tmpdir/Rinst306414111


---------- Making package Biostrings ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making CharBuffer.d from CharBuffer.c
making IntBuffer.d from IntBuffer.c
making R_init_Biostrings.d from R_init_Biostrings.c
making char_frequency.d from char_frequency.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 reverseComplement.d from reverseComplement.c
making utils.d from utils.c
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c CharBuffer.c -o CharBuffer.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c IntBuffer.c -o IntBuffer.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c char_frequency.c -o char_frequency.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c match_boyermoore.c -o match_boyermoore.o
match_boyermoore.c: In function `match_boyermoore':
match_boyermoore.c:370: warning: 'i1' might be used uninitialized in this function
match_boyermoore.c:370: warning: 'i2' might be used uninitialized in this function
match_boyermoore.c:370: warning: 'j1' might be used uninitialized in this function
match_boyermoore.c:371: warning: 'c' might be used uninitialized in this function
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c match_naive.c -o match_naive.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c match_shiftor.c -o match_shiftor.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c reverseComplement.c -o reverseComplement.o
gcc   -Ie:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c utils.c -o utils.o
utils.c: In function `Biostrings_translate_charcpy_from_i1i2':
utils.c:226: warning: 'lkup_val' might be used uninitialized in this function
utils.c: In function `Biostrings_translate_charcpy_from_subset':
utils.c:265: warning: 'lkup_val' might be used uninitialized in this function
utils.c: In function `Biostrings_translate_charcpy_to_i1i2':
utils.c:305: warning: 'lkup_val' might be used uninitialized in this function
utils.c: In function `Biostrings_translate_charcpy_to_subset':
utils.c:344: warning: 'lkup_val' might be used uninitialized in this function
utils.c: In function `Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:421: warning: 'lkup_val' might be used uninitialized in this function
windres -I e:/biocbld/bbs-2.0-bioc/R/include  -i Biostrings_res.rc -o Biostrings_res.o
gcc  -shared -s  -o Biostrings.dll Biostrings.def CharBuffer.o IntBuffer.o R_init_Biostrings.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o reverseComplement.o utils.o Biostrings_res.o  -Le:/biocbld/bbs-2.0-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  save image
Creating a new generic function for "as.integer" in "Biostrings"
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 messages:
1: in the method signature for function "BStringViews" no definition for class: "file" in: matchSignature(signature, fdef, where) 
2: in the method signature for function "eq" no definition for class: "BioString" in: matchSignature(signature, fdef, where) 
  installing inst files
  installing data files
  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
  BString-class                     text    html    latex   example chm
  BStringViews-class                text    html    latex           chm
  BStringViews-constructors         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
  IUPAC_CODE_MAP                    text    html    latex   example chm
  RNAString-class                   text    html    latex   example chm
  alphabetFrequency                 text    html    latex   example chm
  blosum50                          text    html    latex   example chm
  gregexpr2                         text    html    latex   example chm
  matchPattern                      text    html    latex   example chm
  matchProbePair                    text    html    latex   example chm
  needwunsQS                        text    html    latex   example chm
  readFASTA                         text    html    latex   example chm
  reverseComplement                 text    html    latex   example chm
  toComplex                         text    html    latex   example chm
  yeastSEQCHR1                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.0-biocLite\meat\Biostrings\chm\Biostrings.chm





Compile time: 0 minutes, 1 second

21	Topics

262	Local links

1	Internet link

1	Graphic





Created e:\biocbld\bbs-2.0-biocLite\meat\Biostrings\chm\Biostrings.chm, 41,075 bytes

Compression decreased file by 67,901 bytes.

  adding MD5 sums

* DONE (Biostrings)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'Biostrings_2.4.2.tar.gz'
Biostrings

2.4.2

Command output
