BioC 2.10: CHECK report for plier on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/plier.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plier/DESCRIPTION’ ... OK
* this is package ‘plier’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘plier’ can be installed ... OK
* checking installed package size ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: justPlier.Rd:50-52: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/plier.Rcheck/plier/libs/plier.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Object: ‘rwrapper.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘rwrapper.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... NONE
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/plier.Rcheck/00check.log’
for details.

* installing *source* package ‘plier’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c affyplier.cpp -o affyplier.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c plier_impl.cpp -o plier_impl.o
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -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:910:9: warning: ‘LogLikelihood’ may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:49:12: warning: ‘g_ErrorCode’ defined but not used
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rwrapper.cpp -o rwrapper.o
g++ -shared -L/usr/local/lib64 -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/plier.Rcheck/plier/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (plier)

Summary

Command output