Package: Biostrings

Version: 2.1.6

Command: /home/biocbuild/1.9d/R/bin/R CMD check Biostrings_2.1.6.tar.gz

RetCode: 0

Time: 44.5 seconds

Status: WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/home/biocbuild/1.9d/Rpacks/Biostrings.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.1.6'
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 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, base_values)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    base_values
  Mismatches in argument names:
    Position: 2 Code: ... Docs: base_values

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'as.complex'
  x base_values
Objects in \usage without \alias in documentation object 'as.complex':
  as.complex

Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 were 2 warnings, see
  /home/biocbuild/1.9d/Rpacks/Biostrings.Rcheck/00check.log
for details

* Installing *source* package 'Biostrings' ...
** libs
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c alphabetFrequency.c -o alphabetFrequency.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c bbuf.c -o bbuf.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c ibuf.c -o ibuf.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c reverseComplement.c -o reverseComplement.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c shiftor.c -o shiftor.o
shiftor.c: In function 'shiftor':
shiftor.c:224: warning: 'index' may be used uninitialized in this function
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include  -I/usr/local/include    -fpic  -g -O2 -std=gnu99 -Wall -c utils.c -o utils.o
utils.c: In function 'Biostrings_translate_charcpy_from_subset':
utils.c:261: warning: unused variable 'b'
utils.c: In function 'Biostrings_translate_charcpy_to_subset':
utils.c:344: warning: unused variable 'b'
gcc -shared -L/usr/local/lib64 -o Biostrings.so alphabetFrequency.o bbuf.o ibuf.o reverseComplement.o R_init_Biostrings.o shiftor.o utils.o   
** 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 message:
in the method signature for function 'BStringViews' no definition for class: "file" in: matchSignature(signature, fdef, where) 
** help
 >>> Building/Updating help pages for package 'Biostrings'
     Formats: text html latex example 
  BString-class                     text    html    latex   example
  BStringViews-class                text    html    latex   example
  Biostrings-internals              text    html    latex
  alphabetFrequency                 text    html    latex   example
  as.complex                        text    html    latex   example
  blosum50                          text    html    latex   example
  matchPattern                      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)