Package: MANOR

Version: 1.6.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check MANOR_1.6.0.tar.gz

RetCode: 0

Time: 149.4 seconds

Status: OK

CheckDir: MANOR.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/MANOR.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.6.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MANOR' 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 non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 ... OK
* checking Rd cross-references ... 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
* checking for portable use of $BLAS_LIBS ... OK
* creating MANOR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating MANOR-manual.tex ... OK
* checking MANOR-manual.tex ... OK

* Installing *source* package 'MANOR' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function 'nem':
Rnem_exe.c:178: warning: 'tmpV' is used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c exememo.c -o exememo.o
exememo.c: In function 'GenAlloc':
exememo.c:39: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
exememo.c:39: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'maxcols' may be used uninitialized in this function
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_alg.c -o nem_alg.o
nem_alg.c:85:1: warning: "MAXFLOAT" redefined
In file included from nem_alg.c:73:
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/include/math.h:87:1: warning: this is the location of the previous definition
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_mod.c -o nem_mod.o
nem_mod.c:51:1: warning: "MAXFLOAT" redefined
In file included from nem_mod.c:39:
/usr/local/lib/gcc/sparc-sun-solaris2.9/4.1.1/include/math.h:87:1: warning: this is the location of the previous definition
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_nei.c -o nem_nei.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include  -I/usr/local/include    -fPIC  -g -O2 -std=gnu99 -Wall -c nem_ver.c -o nem_ver.o
gcc -G -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o   
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GLAD
[1] "Have fun with GLAD"
** help
 >>> Building/Updating help pages for package 'MANOR'
     Formats: text html latex example 
  MANOR-internal                    text    html    latex
  arrayTrend                        text    html    latex   example
  detectSB                          text    html    latex   example
  flag                              text    html    latex   example
  flag.arrayCGH                     text    html    latex   example
  flag.summary                      text    html    latex   example
  flags                             text    html    latex   example
  genome.plot                       text    html    latex   example
  html.report                       text    html    latex   example
  import                            text    html    latex   example
  nem                               text    html    latex   example
  norm.arrayCGH                     text    html    latex   example
  qscore                            text    html    latex   example
  qscore.arrayCGH                   text    html    latex   example
  qscore.summary                    text    html    latex   example
  qscores                           text    html    latex   example
  report.plot                       text    html    latex   example
  sort.arrayCGH                     text    html    latex   example
  spatial                           text    html    latex   example
** building package indices ...
* DONE (MANOR)