Package: Biostrings

Version: 2.4.1

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD build Biostrings

RetCode: 0

Time: 96.9 seconds

Status: OK

PackageFile: Biostrings_2.4.1.tar.gz

* 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/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c CharBuffer.c -o CharBuffer.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c IntBuffer.c -o IntBuffer.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-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/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c char_frequency.c -o char_frequency.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -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: 'c' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'j1' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'i2' may be used uninitialized in this function
match_boyermoore.c:370: warning: 'i1' may be used uninitialized in this function
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c match_naive.c -o match_naive.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c match_shiftor.c -o match_shiftor.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c reverseComplement.c -o reverseComplement.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-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:462: warning: 'lkup_val.r' may be used uninitialized in this function
utils.c:462: warning: 'lkup_val.i' may be used uninitialized in this function
utils.c: In function 'Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:421: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_to_subset':
utils.c:344: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_to_i1i2':
utils.c:305: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_from_subset':
utils.c:265: warning: 'lkup_val' may be used uninitialized in this function
utils.c: In function 'Biostrings_translate_charcpy_from_i1i2':
utils.c:226: warning: 'lkup_val' may be used uninitialized in this function
gcc -std=gnu99 -G -L/usr/local/lib -o Biostrings.so CharBuffer.o IntBuffer.o R_init_Biostrings.o char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o reverseComplement.o utils.o   -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** 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.complex" 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) 
** 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
  BStringViews-class                text    html    latex
  BStringViews-constructors         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
  as.complex                        text    html    latex   example
  blosum50                          text    html    latex   example
  gregexpr2                         text    html    latex   example
  matchPattern                      text    html    latex   example
  matchProbePair                    text    html    latex   example
  needwunsQS                        text    html    latex   example
  readFASTA                         text    html    latex   example
  reverseComplement                 text    html    latex   example
  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 files
* checking for empty or unneeded directories
* building 'Biostrings_2.4.1.tar.gz'