Package: fbat

Version: 1.1.2

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check fbat_1.1.2.tar.gz

RetCode: 0

Time: 30.5 seconds

Status: WARNINGS

CheckDir: fbat.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/fbat.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'fbat/DESCRIPTION' ... OK
* this is package 'fbat' version '1.1.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'fbat' can be installed ... WARNING
Found the following significant warnings:
  WARNING: true value of 'SaveImage' is deprecated in favour of 'LazyLoad: true'
See '/home/biocbuild/bbs-2.1-bioc/meat/fbat.Rcheck/00install.out' for details.
* 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
readHapMap: no visible binding for global variable 'sampleInfoCEU'
readHapMap: no visible binding for global variable 'sampleInfoYRI'
readHapMap: no visible binding for global variable 'sampleInfoCHB'
readHapMap: no visible binding for global variable 'sampleInfoJPT'
* 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 data for non-ASCII characters ... 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 fbat-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating fbat-manual.tex ... OK
* checking fbat-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/fbat.Rcheck/00check.log
for details

* Installing *source* package 'fbat' ...
** 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 FBAT.c -o FBAT.o
FBAT.c: In function 'countLines':
FBAT.c:2142: warning: 'tmpnc2' may be used uninitialized in this function
FBAT.c: In function 'oneNuclearFamily':
FBAT.c:1859: warning: 'sex2' may be used uninitialized in this function
FBAT.c:1859: warning: 'sex1' may be used uninitialized in this function
FBAT.c: In function 'decomposePed':
FBAT.c:1986: warning: 'i' may be used uninitialized in this function
FBAT.c: In function 'checkoneNuclearFamily':
FBAT.c:1667: warning: 'sex2' may be used uninitialized in this function
FBAT.c:1667: warning: 'sex1' may be used uninitialized in this function
FBAT.c: In function 'checkdecomposePed':
FBAT.c:1590: warning: 'i' may be used uninitialized in this function
FBAT.c: In function 'checkCompatible':
FBAT.c:1404: warning: 'start2' may be used uninitialized in this function
FBAT.c: In function 'fbat':
FBAT.c:43: warning: 'start2' may be used uninitialized in this function
gfortran   -fpic  -g -O2 -Wall -c missGFreq.f -o missGFreq.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 register.c -o register.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o fbat.so FBAT.o missGFreq.o register.o  -lgfortran -lm -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
WARNING: true value of 'SaveImage' is deprecated in favour of 'LazyLoad: true'
** save image
Loading required package: MASS
Loading required package: GeneticsBase
Loading required package: combinat

Attaching package: 'combinat'


	The following object(s) are masked from package:utils :

	 combn 

Loading required package: xtable
Loading required package: mvtnorm
** help
Note: unmatched right brace in 'getFounders' on or after line 6
 >>> Building/Updating help pages for package 'fbat'
     Formats: text html latex example 
  checkMarkers                      text    html    latex   example
  checkMendelian                    text    html    latex   example
  fbat                              text    html    latex   example
  getFounders                       text    html    latex   example
  missGFreq                         text    html    latex   example
  pedAFreq                          text    html    latex   example
  pedFlagHomo                       text    html    latex   example
  pedGFreq                          text    html    latex   example
  pedHardyWeinberg                  text    html    latex   example
  readHapMap                        text    html    latex   example
  readLink                          text    html    latex   example
  readPed                           text    html    latex   example
  sampleInfoCEU                     text    html    latex   example
  sampleInfoCHB                     text    html    latex   example
  sampleInfoJPT                     text    html    latex   example
  sampleInfoYRI                     text    html    latex   example
  summaryPvalue                     text    html    latex   example
  viewFlagHomo                      text    html    latex   example
  viewHW                            text    html    latex   example
  viewstat                          text    html    latex   example
** building package indices ...
* DONE (fbat)