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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: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes MANOR_1.14.0.tar.gz
StartedAt: 2009-04-18 19:17:46 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 19:18:45 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 58.6 seconds
RetCode: 0
Status: OK
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/MANOR.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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 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 R.css in E:/biocbld/bbs-2.3-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  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c Rnem_arg.c -o Rnem_arg.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c Rnem_exe.c -o Rnem_exe.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -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  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -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  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_alg.c -o nem_alg.o
nem_alg.c: In function 'ClassifyByNemOneBeta':
nem_alg.c:1626: warning: 'bestCritS.Errcur.Errorrate' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Errorrate' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Ibestpermut' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Ibestpermut' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Loclas_N_Kc' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Loclas_N_Kc' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errcur.Agree_Km_Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errcur.Agree_Km_Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Perm_Kmfac_Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Perm_Kmfac_Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Refclas_N_Kr' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Refclas_N_Kr' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.TieRule' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.TieRule' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kmfac' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kmfac' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Km' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Km' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kr' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kr' was declared here
nem_alg.c:1626: warning: 'bestCritS.Errinfo.Kc' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Errinfo.Kc' was declared here
nem_alg.c:1626: warning: 'bestCritS.Z' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.Z' was declared here
nem_alg.c:1626: warning: 'bestCritS.G' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.G' was declared here
nem_alg.c:1626: warning: 'bestCritS.U' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.U' was declared here
nem_alg.c:1626: warning: 'bestCritS.M' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.M' was declared here
nem_alg.c:1626: warning: 'bestCritS.D' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.D' was declared here
nem_alg.c:1626: warning: 'bestCritS.L' may be used uninitialized in this function
nem_alg.c:1626: note: 'bestCritS.L' was declared here
nem_alg.c:1631: warning: 'bestbeta' may be used uninitialized in this function
nem_alg.c:1631: note: 'bestbeta' was declared here
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_hlp.c -o nem_hlp.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_mod.c -o nem_mod.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_nei.c -o nem_nei.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_rnd.c -o nem_rnd.o
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.3-bioc/R/include     -O3 -Wall  -c nem_ver.c -o nem_ver.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include  -i MANOR_res.rc -o MANOR_res.o
gcc  -std=gnu99  -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-2.3-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package MANOR for lazy loading
Loading required package: GLAD
  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
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
Note: ignoring empty \keyword entries in file 'arrayTrend.Rd'
  arrayTrend                        text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
Note: ignoring empty \keyword entries in file 'detectSB.Rd'
  detectSB                          text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'flag.Rd'
Note: ignoring empty \keyword entries in file 'flag.Rd'
  flag                              text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'flag.arrayCGH.Rd'
  flag.arrayCGH                     text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
Note: ignoring empty \keyword entries in file 'flag.summary.Rd'
  flag.summary                      text    html    latex   example chm
  flags                             text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
Note: ignoring empty \keyword entries in file 'genome.plot.Rd'
  genome.plot                       text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'html.report.Rd'
Note: removing empty section \examples in file 'html.report.Rd'
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           chm
Note: ignoring empty \keyword entries in file 'import.Rd'
Note: ignoring empty \keyword entries in file 'import.Rd'
  import                            text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'nem.Rd'
Note: ignoring empty \keyword entries in file 'nem.Rd'
  nem                               text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'norm.arrayCGH.Rd'
  norm.arrayCGH                     text    html    latex   example chm
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'
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           chm
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'qscore.arrayCGH.Rd'
  qscore.arrayCGH                   text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
Note: ignoring empty \keyword entries in file 'qscore.summary.Rd'
  qscore.summary                    text    html    latex   example chm
  qscores                           text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
Note: ignoring empty \keyword entries in file 'report.plot.Rd'
  report.plot                       text    html    latex   example chm
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
Note: ignoring empty \keyword entries in file 'sort.arrayCGH.Rd'
  sort.arrayCGH                     text    html    latex   example chm
  spatial                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm


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


Created e:\biocbld\bbs-2.3-bioc\meat\MANOR.Rcheck\00_pkg_src\MANOR\chm\MANOR.chm, 50,450 bytes
Compression decreased file by 62,403 bytes.
  adding MD5 sums

* DONE (MANOR)