Package: SAGx

Version: 1.11.3

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check SAGx_1.11.3.tar.gz

RetCode: 0

Time: 68.5 seconds

Status: OK

CheckDir: SAGx.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/SAGx.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'SAGx/DESCRIPTION' ... OK
* this is package 'SAGx' version '1.11.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SAGx' 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 whether the name space 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
clin2mim: no visible binding for global variable 'dbs'
clin2mim: no visible binding for global variable 'clinical'
estimatep0: no visible binding for global variable 'pp'
fetchSignal: no visible global function definition for 'sqlQuery'
fp.fn: no visible binding for global variable 'pvals'
Fstat: no visible binding for global variable 'M'
gap: no visible binding for global variable 'g'
GSEA.mean.t: no visible binding for global variable 'samroc.res'
GSEA.mean.t: no visible binding for global variable 'kegg'
GSEA.mean.t : maxmeanf: no visible binding for global variable
  'plustat'
list.experiments: no visible global function definition for 'sqlQuery'
mat2TeX: no visible global function definition for 'errif'
p0.mom: no visible binding for global variable 'pvalues'
pava.fdr: no visible binding for global variable 'pvalues'
R2BASE: no visible binding for global variable 'clingen'
R2BASE: no visible binding for global variable 'AZID'
R2BASE: no visible binding for global variable 'dats'
R2BASE: no visible binding for global variable 'annots'
R2mim: no visible binding for global variable 'inm'
rank.genes: no visible binding for global variable 'indats'
rank.trend: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'x'
rsd.test: no visible binding for global variable 'y'
samrocN: no visible binding for global variable 'M'
samrocNboot: no visible binding for global variable 'M'
Xprep: no visible binding for global variable 'M'
Xprep.resid: no visible binding for global variable 'M'
* 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 SAGx-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating SAGx-manual.tex ... OK
* checking SAGx-manual.tex ... OK

* Installing *source* package 'SAGx' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c newboot.c -o newboot.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c samrocNboot.c -o samrocNboot.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o SAGx.so minigsea.o newboot.o samrocNboot.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: multtest
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: survival
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'SAGx'
     Formats: text html latex example 
  Fstat                             text    html    latex   example
  GSEA.mean.t                       text    html    latex
  JT.test                           text    html    latex   example
  R2BASE                            text    html    latex
  R2mim                             text    html    latex
  Xprep                             text    html    latex
  Xprep.resid                       text    html    latex
  clin2mim                          text    html    latex
  cluster.q                         text    html    latex
  estimatep0                        text    html    latex
  fetchSignal                       text    html    latex   example
  firstpass                         text    html    latex   example
  fom                               text    html    latex
  fp.fn                             text    html    latex
  gap                               text    html    latex   example
  list.experiments                  text    html    latex   example
  list.intersection.p               text    html    latex
  mat2TeX                           text    html    latex
  myclus                            text    html    latex   example
  normalise                         text    html    latex
  one.probeset.per.gene             text    html    latex
  outlier                           text    html    latex   example
  p0.mom                            text    html    latex
  pava.fdr                          text    html    latex
  pava                              text    html    latex   example
  rank.genes                        text    html    latex
  rank.trend                        text    html    latex   example
  rsd.test                          text    html    latex
  samroc.result-class               text    html    latex
  samrocn                           text    html    latex
  samrocnboot                       text    html    latex   example
  union.of.pways                    text    html    latex   example
** building package indices ...
* DONE (SAGx)