Package: plier

Version: 1.7.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check plier_1.7.0.tar.gz

RetCode: 0

Time: 74.8 seconds

Status: OK

CheckDir: plier.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/plier.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'plier/DESCRIPTION' ... OK
* this is package 'plier' version '1.7.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'plier' 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 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 ... NOTE
Found possibly global 'T' or 'F' in the following functions:
  justPlier .testoneprobeset
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating plier-Ex.R ... OK
* checking examples ... OK
* creating plier-manual.tex ... OK
* checking plier-manual.tex ... OK

* Installing *source* package 'plier' ...
** libs
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c affyplier.cpp -o affyplier.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function `long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:909: warning: `double LogLikelihood' might be used uninitialized 
   in this function
plieralg.cpp: At top level:
plieralg.cpp:48: warning: `int g_ErrorCode' defined but not used
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c plier_impl.cpp -o plier_impl.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp: In function `void one_probeset(bool*, double*, double*, double*, 
   double*, double*, double*, double*, double*, int*, double*, int*, bool*, 
   bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, 
   double*, double*, double*, int*)':
rwrapper.cpp:159: warning: `long int*rpct' might be used uninitialized in this 
   function
g++ -shared -L/usr/local/lib -o plier.so affyplier.o plieralg.o plier_impl.o rwrapper.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** help
 >>> Building/Updating help pages for package 'plier'
     Formats: text html latex example 
  justPlier                         text    html    latex   example
** building package indices ...
* DONE (plier)