Package: gaga

Version: 1.12.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings gaga_1.12.0.tar.gz

StartedAt: 2011-10-20 12:42:51 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 12:43:23 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 32.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gaga.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/gaga.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘gaga’ can be installed ... WARNING
Found the following significant warnings:
  Warning: LazyLoad = FALSE is deprecated
See ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/gaga.Rcheck/00install.out’ for details.
* 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: checkfit.Rd:61-63: Dropping empty section \examples
prepare_Rd: dcgamma.Rd:53-54: Dropping empty section \examples
prepare_Rd: getpar.Rd:37-38: Dropping empty section \examples
prepare_Rd: posmeansGG.Rd:54-55: Dropping empty section \examples
prepare_Rd: powclasspred.Rd:66-67: Dropping empty section \examples
prepare_Rd: print.gagaclus.Rd:17-18: Dropping empty section \details
prepare_Rd: print.gagahyp.Rd:19-20: Dropping empty section \details
prepare_Rd: simnewsamples.Rd:45-46: 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/gaga.Rcheck/00check.log’
for details

* installing *source* package ‘gaga’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cseqdesma.c -o cseqdesma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cstat.c -o cstat.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o gaga.so cseqdesma.o cstat.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/gaga.Rcheck/gaga/libs
** R
** inst
Warning: LazyLoad = FALSE is deprecated
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (gaga)

name	user	system	elapsed
classpred	0	0	0
findgenes	0	0	0
fitGG	0.252	0.008	0.261
geneclus	0	0	0
parest	0	0	0
simGG	0	0	0