Package: Biostrings

Version: 2.1.6

Command: E:\hpages\1.9d\R\bin\R.exe CMD check Biostrings_2.1.6.tar.gz

RetCode: 0

Time: 95.8 seconds

Status: WARNINGS

CheckDir: Biostrings.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory 'E:/hpages/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 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
  E:/hpages/1.9d/Rpacks/Biostrings.Rcheck/00check.log
for details

installing R.css in E:/hpages/1.9d/Rpacks/Biostrings.Rcheck


---------- Making package Biostrings ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making R_init_Biostrings.d from R_init_Biostrings.c
making alphabetFrequency.d from alphabetFrequency.c
making bbuf.d from bbuf.c
making ibuf.d from ibuf.c
making reverseComplement.d from reverseComplement.c
making shiftor.d from shiftor.c
making utils.d from utils.c
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c alphabetFrequency.c -o alphabetFrequency.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c bbuf.c -o bbuf.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c ibuf.c -o ibuf.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c reverseComplement.c -o reverseComplement.o
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -c shiftor.c -o shiftor.o
shiftor.c: In function `shiftor':
shiftor.c:224: warning: 'index' might be used uninitialized in this function
gcc   -Ie:/hpages/1.9d/R/include  -Wall -O2 -std=gnu99   -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'
windres --include-dir e:/hpages/1.9d/R/include  -i Biostrings_res.rc -o Biostrings_res.o
gcc  -shared -s  -o Biostrings.dll Biostrings.def R_init_Biostrings.o alphabetFrequency.o bbuf.o ibuf.o reverseComplement.o shiftor.o utils.o Biostrings_res.o  -Le:/hpages/1.9d/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.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) 
  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 
  BString-class                     text    html    latex   example chm
  BStringViews-class                text    html    latex   example chm
  Biostrings-internals              text    html    latex           chm
  alphabetFrequency                 text    html    latex   example chm
  as.complex                        text    html    latex   example chm
  blosum50                          text    html    latex   example chm
  matchPattern                      text    html    latex   example chm
  needwunsQS                        text    html    latex   example chm
  readFASTA                         text    html    latex   example chm
  reverseComplement                 text    html    latex   example chm
  yeastSEQCHR1                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\hpages\1.9d\Rpacks\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm


Compile time: 0 minutes, 0 seconds
12	Topics
203	Local links
1	Internet link
1	Graphic


Created e:\hpages\1.9d\Rpacks\Biostrings.Rcheck\00_pkg_src\Biostrings\chm\Biostrings.chm, 31,925 bytes
Compression decreased file by 47,257 bytes.
  adding MD5 sums

* DONE (Biostrings)