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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 135/247HostnameOSArchBUILDCHECKBUILD BIN

MANOR

1.9.4

Pierre Neuvial
Last Changed Date: 2007-06-19 07:39:13 -0700
Last Changed Rev: 25474
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK [ OK ] OK 
pitt Mac OS X (10.4.10) i386  OK  OK  OK 
Package: MANOR
Version: 1.9.4
Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check MANOR_1.9.4.tar.gz
RetCode: 0
Time: 62.3 seconds
Status: OK
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/MANOR.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.9.4'
* 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 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 ... NOTE
getChromosomeArm: no visible binding for global variable 'cytoband'
w: no visible binding for global variable 'fh'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'arrayTrend':
  arrayTrend.default arrayTrend.arrayCGH

S3 methods shown with full name in documentation object 'detectSB':
  detectSB.arrayCGH

S3 methods shown with full name in documentation object 'flag.summary':
  flag.summary.arrayCGH flag.summary.default

S3 methods shown with full name in documentation object 'genome.plot':
  genome.plot.arrayCGH genome.plot.default

S3 methods shown with full name in documentation object 'html.report':
  html.report.arrayCGH html.report.default

S3 methods shown with full name in documentation object 'nem':
  nem.default nem.arrayCGH

S3 methods shown with full name in documentation object 'report.plot':
  report.plot.arrayCGH report.plot.default

S3 methods shown with full name in documentation object 'sort.arrayCGH':
  sort.arrayCGH

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 ... OK

MANOR.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/MANOR.Rcheck


---------- Making package MANOR ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making Rnem_arg.d from Rnem_arg.c
making Rnem_exe.d from Rnem_exe.c
making exememo.d from exememo.c
making lib_io.d from lib_io.c
making nem_alg.d from nem_alg.c
making nem_hlp.d from nem_hlp.c
making nem_mod.d from nem_mod.c
making nem_nei.d from nem_nei.c
making nem_rnd.d from nem_rnd.c
making nem_ver.d from nem_ver.c
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c Rnem_arg.c -o Rnem_arg.o
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c Rnem_exe.c -o Rnem_exe.o
Rnem_exe.c: In function `nem':
Rnem_exe.c:168: warning: 'tmpV' might be used uninitialized in this function
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c exememo.c -o exememo.o
exememo.c: In function `GenAlloc':
exememo.c:39: warning: long int format, size_t arg (arg 5)
exememo.c:39: warning: long int format, size_t arg (arg 6)
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c lib_io.c -o lib_io.o
lib_io.c: In function `CountLinesColumns':
lib_io.c:354: warning: 'mincols' might be used uninitialized in this function
lib_io.c:354: warning: 'maxcols' might be used uninitialized in this function
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_alg.c -o nem_alg.o
nem_alg.c: In function `ClassifyByNemOneBeta':
nem_alg.c:1631: warning: 'bestbeta' might be used uninitialized in this function
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_hlp.c -o nem_hlp.o
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_mod.c -o nem_mod.o
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_nei.c -o nem_nei.o
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_rnd.c -o nem_rnd.o
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c nem_ver.c -o nem_ver.o
windres -I e:/biocbld/bbs-2.1-bioc/R/include  -i MANOR_res.rc -o MANOR_res.o
gcc  -shared -s  -o MANOR.dll MANOR.def 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 MANOR_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'MANOR'
     Formats: text html latex example chm 
  MANOR-internal                    text    html    latex           chm
  arrayTrend                        text    html    latex   example chm
  detectSB                          text    html    latex   example chm
  flag                              text    html    latex   example chm
  flag.arrayCGH                     text    html    latex   example chm
  flag.summary                      text    html    latex   example chm
  flags                             text    html    latex   example chm
  genome.plot                       text    html    latex   example chm
  html.report                       text    html    latex   example chm
  import                            text    html    latex   example chm
  nem                               text    html    latex   example chm
  norm.arrayCGH                     text    html    latex   example chm
  qscore                            text    html    latex   example chm
  qscore.arrayCGH                   text    html    latex   example chm
  qscore.summary                    text    html    latex   example chm
  qscores                           text    html    latex   example chm
  report.plot                       text    html    latex   example chm
  sort.arrayCGH                     text    html    latex   example chm
  spatial                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm


Compile time: 0 minutes, 0 seconds
20	Topics
121	Local links
20	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm, 50,272 bytes
Compression decreased file by 62,282 bytes.
  preparing package MANOR for lazy loading
Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
  adding MD5 sums

* DONE (MANOR)