Package: Biostrings

Version: 2.4.1

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check Biostrings_2.4.1.tar.gz

RetCode: 0

Time: 160.8 seconds

Status: WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.0-bioc/meat/Biostrings.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.4.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biostrings' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'as.complex':
as.complex
  Code: function(x, ...)
  Docs: function(x, baseValues)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    baseValues
  Mismatches in argument names:
    Position: 2 Code: ... Docs: baseValues

* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Biostrings-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Biostrings-manual.tex ... OK
* checking Biostrings-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/bbs-2.0-bioc/meat/Biostrings.Rcheck/00check.log
for details

* 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 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 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 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 -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 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 utils.c -o utils.o
utils.c: In function `Biostrings_reverse_translate_charcpy_from_i1i2':
utils.c:421: 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_translate_charcpy_to_i1i2':
utils.c:305: 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_from_i1i2':
utils.c:226: warning: `lkup_val' might be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib -o Biostrings.so CharBuffer.o char_frequency.o IntBuffer.o match_boyermoore.o match_naive.o match_shiftor.o reverseComplement.o R_init_Biostrings.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)