Package: msbase

Version: 1.5.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check msbase_1.5.0.tar.gz

RetCode: 0

Time: 163.2 seconds

Status: WARNINGS

CheckDir: msbase.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/msbase.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-06-04 r38279)
* checking for file 'msbase/DESCRIPTION' ... OK
* this is package 'msbase' version '1.5.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'msbase' 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 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
* checking for portable compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CFLAGS':
  -ansi
* creating msbase-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating msbase-manual.tex ... OK
* checking msbase-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.9d/Rpacks/msbase.Rcheck/00check.log
for details

* Installing *source* package 'msbase' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include  -ansi -g -fPIC  -g -O2 -std=gnu99 -Wall -c llogic.c -o llogic.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include  -ansi -g -fPIC  -g -O2 -std=gnu99 -Wall -c mscalibD.c -o mscalibD.o
mscalibD.c: In function `getaccDIFUS':
mscalibD.c:521: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -G -L/usr/local/lib -o msbase.so llogic.o mscalibD.o   
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: MASS
Loading required package: XML
Creating a new generic function for 'subset' in 'msbase'
Creating a new generic function for 'image' in 'msbase'
Creating a new generic function for 'summary' in 'msbase'
Creating a new generic function for 'plot' in 'msbase'
Creating a new generic function for 'points' in 'msbase'
[1] "test1"
Creating a new generic function for 'unlist' in 'msbase'
Creating a new generic function for 'hist' in 'msbase'
** help
 >>> Building/Updating help pages for package 'msbase'
     Formats: text html latex example 
  List                              text    html    latex   example
  Massvector-class                  text    html    latex   example
  Massvectorlist-class              text    html    latex   example
  Mlist-class                       text    html    latex   example
  ROCDATA                           text    html    latex   example
  cals-methods                      text    html    latex   example
  calssim                           text    html    latex   example
  fbinary-methods                   text    html    latex   example
  fcor-methods                      text    html    latex   example
  fdist-methods                     text    html    latex   example
  finterS-methods                   text    html    latex   example
  fintersect-methods                text    html    latex   example
  fis.element-methods               text    html    latex   example
  fmatch-methods                    text    html    latex   example
  fmatchall-methods                 text    html    latex   example
  fsetdiff-methods                  text    html    latex   example
  fsetequal-methods                 text    html    latex   example
  funion-methods                    text    html    latex   example
  gamasses-methods                  text    html    latex   example
  listdist-methods                  text    html    latex
  nrmatch-methods                   text    html    latex   example
  numeric-class                     text    html    latex   example
  pldata                            text    html    latex   example
  undocument-internal               text    html    latex
** building package indices ...
* DONE (msbase)