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Package 165/294HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.14.0
Pierre Neuvial
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/MANOR
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: MANOR
Version: 1.14.0
Command: /home/biocbuild/bbs-2.3-bioc/R/bin/R CMD check --no-vignettes MANOR_1.14.0.tar.gz
StartedAt: 2009-04-18 15:56:50 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 15:57:18 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 28.6 seconds
RetCode: 0
Status: OK
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/MANOR.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.14.0'
* 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 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 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 ... 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 MANOR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating MANOR-manual.tex ... OK
* checking MANOR-manual.tex using pdflatex ... OK

MANOR.Rcheck/00install.out:

* Installing *source* package 'MANOR' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c exememo.c -o exememo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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 -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_alg.c -o nem_alg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_mod.c -o nem_mod.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_nei.c -o nem_nei.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nem_ver.c -o nem_ver.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function ‘MakeErrinfo’:
Rnem_exe.c:216: warning: cast from pointer to integer of different size
gcc -std=gnu99 -shared -L/usr/local/lib64 -o MANOR.so exememo.o lib_io.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o Rnem_arg.o Rnem_exe.o   -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** 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
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
  arrayTrend                        text    html    latex   example
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
  detectSB                          text    html    latex   example
Note: ignoring empty \keyword entries in file 'flag.Rd'
  flag                              text    html    latex   example
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
  flag.arrayCGH                     text    html    latex   example
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
  flag.summary                      text    html    latex   example
  flags                             text    html    latex   example
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
  genome.plot                       text    html    latex   example
Note: ignoring empty \keyword entries in file 'html.report.Rd'
Note: removing empty section \examples in file 'html.report.Rd'
  html.report                       text    html    latex
Note: ignoring empty \keyword entries in file 'import.Rd'
  import                            text    html    latex   example
Note: ignoring empty \keyword entries in file 'nem.Rd'
  nem                               text    html    latex   example
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
  norm.arrayCGH                     text    html    latex   example
Note: ignoring empty \keyword entries in file 'qscore.Rd'
Note: removing empty section \details in file 'qscore.Rd'
Note: removing empty section \examples in file 'qscore.Rd'
  qscore                            text    html    latex
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
  qscore.arrayCGH                   text    html    latex   example
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
  qscore.summary                    text    html    latex   example
  qscores                           text    html    latex   example
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
  report.plot                       text    html    latex   example
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
  sort.arrayCGH                     text    html    latex   example
  spatial                           text    html    latex   example
** building package indices ...
* DONE (MANOR)