Package: GLAD

Version: 1.6.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check GLAD_1.6.0.tar.gz

RetCode: 0

Time: 102.8 seconds

Status: OK

CheckDir: GLAD.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/GLAD.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '1.6.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GLAD' 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 syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating GLAD-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GLAD-manual.tex ... OK
* checking GLAD-manual.tex ... OK

* Installing *source* package 'GLAD' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c distance.c -o distance.o
distance.c: In function `R_correlation':
distance.c:175: warning: unused variable `dist'
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -Wall -c glad.cpp -o glad.o
glad.cpp: In function `void detectOutliers(double*, int*, int*, int*, int*, 
   int*, double*, int*)':
glad.cpp:106: warning: comparison between signed and unsigned integer 
   expressions
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c glad-function.c -o glad-function.o
glad-function.c: In function `updateOutliers':
glad-function.c:118: warning: suggest parentheses around comparison in operand of &
glad-function.c: In function `updateOutliersMoveBkp':
glad-function.c:143: warning: suggest parentheses around comparison in operand of &
glad-function.c: In function `moveBkp':
glad-function.c:174: warning: suggest parentheses around comparison in operand of &
glad-function.c:174: warning: suggest parentheses around comparison in operand of &
glad-function.c:174: warning: suggest parentheses around comparison in operand of &
glad-function.c:185: warning: suggest parentheses around comparison in operand of &
glad-function.c:185: warning: suggest parentheses around comparison in operand of &
glad-function.c:185: warning: suggest parentheses around comparison in operand of &
glad-function.c:185: warning: suggest parentheses around comparison in operand of &
glad-function.c: In function `awsBkp':
glad-function.c:231: warning: suggest parentheses around comparison in operand of &
glad-function.c:231: warning: suggest parentheses around comparison in operand of &
glad-function.c:231: warning: suggest parentheses around comparison in operand of &
glad-function.c:259: warning: suggest parentheses around comparison in operand of &
glad-function.c:261: warning: suggest parentheses around comparison in operand of |
glad-function.c: In function `updateBkpRL':
glad-function.c:333: warning: suggest parentheses around comparison in operand of |
glad-function.c:367: warning: suggest parentheses around comparison in operand of &
glad-function.c:367: warning: suggest parentheses around comparison in operand of &
glad-function.c:377: warning: suggest parentheses around comparison in operand of &
glad-function.c: In function `updateGNL':
glad-function.c:543: warning: suggest parentheses around comparison in operand of |
glad-function.c:556: warning: suggest parentheses around comparison in operand of |
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c hclust.c -o hclust.o
hclust.c: In function `hclust':
hclust.c:56: warning: unused variable `tmp'
hclust.c:276: warning: control reaches end of non-void function
hclust.c:49: warning: `im' might be used uninitialized in this function
hclust.c:49: warning: `jm' might be used uninitialized in this function
hclust.c:49: warning: `jj' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c laws.c -o laws.o
g++ -shared -L/usr/local/lib64 -o GLAD.so distance.o glad.o glad-function.o hclust.o laws.o   
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'GLAD'
     Formats: text html latex example 
  ChrNumeric                        text    html    latex   example
  ColorBar                          text    html    latex   example
  GLAD-internal                     text    html    latex
  arrayCGH                          text    html    latex   example
  arrayPersp                        text    html    latex   example
  arrayPlot                         text    html    latex   example
  as.data.frame.profileCGH          text    html    latex   example
  as.profileCGH                     text    html    latex   example
  bladder                           text    html    latex   example
  cytoband                          text    html    latex   example
  daglad                            text    html    latex   example
  glad                              text    html    latex   example
  hclust                            text    html    latex   example
  kernel                            text    html    latex
  myPalette                         text    html    latex   example
  plotProfile                       text    html    latex   example
  profileCGH                        text    html    latex   example
  snijders                          text    html    latex   example
  tkdaglad                          text    html    latex   example
  veltman                           text    html    latex   example
** building package indices ...
* DONE (GLAD)