Package: Biostrings

Version: 2.0.3

Command: /loc/biocbuild/1.8d/R/bin/R CMD check Biostrings_2.0.3.tar.gz

RetCode: 0

Time: 87.4 seconds

Status: OK

CheckDir: Biostrings.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/Biostrings.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.0.3'
* 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 library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... 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

* Installing *source* package 'Biostrings' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c alphabetFrequency.c -o alphabetFrequency.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c bbuf.c -o bbuf.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c ibuf.c -o ibuf.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c reverseComplement.c -o reverseComplement.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/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' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/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.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
  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)