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Package 180/319HostnameOS / ArchBUILDCHECKBUILD BIN
MANOR 1.16.0
Pierre Neuvial
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/MANOR
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 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 (10.5.8) / i386  OK  OK  OK 
Package: MANOR
Version: 1.16.0
Command: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes MANOR_1.16.0.tar.gz
StartedAt: 2009-10-20 17:35:24 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:36:17 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 52.3 seconds
RetCode: 0
Status: OK
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/MANOR.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MANOR/DESCRIPTION' ... OK
* this is package 'MANOR' version '1.16.0'
* checking package name space information ... OK
* 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 whether the name space 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 files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

MANOR.Rcheck/00install.out:

* Installing *source* package 'MANOR' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rnem_arg.c -o Rnem_arg.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c Rnem_exe.c -o Rnem_exe.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c lib_io.c -o lib_io.o
lib_io.c: In function 'CountLinesColumns':
lib_io.c:354: warning: 'mincols' may be used uninitialized in this function
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -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
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_hlp.c -o nem_hlp.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_mod.c -o nem_mod.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_nei.c -o nem_nei.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_rnd.c -o nem_rnd.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c nem_ver.c -o nem_ver.o
gcc -shared -s -o MANOR.dll tmp.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 -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** R
** data
** inst
** preparing package for lazy loading
[1] "Have fun with GLAD"
[1] "For smoothing it is possible to use either"
[1] "the AWS algorithm (Polzehl and Spokoiny, 2002)"
[1] "or the HaarSeg algorithm (Ben-Yaacov and Eldar, 2008)"
[1] ""
[1] "If you use the package with AWS, please cite:"
[1] "Hupe et al. (2004) and Polzehl and Spokoiny (2002)"
[1] ""
[1] "If you use the package with HaarSeg, please cite:"
[1] "Hupe et al. (2004) and (Ben-Yaacov and Eldar, 2008)"
** help
*** installing help indices
 >>> 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.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           chm
  import                            text    html    latex   example chm
  nem                               text    html    latex   example chm
  norm                              text    html    latex   example chm
  qscore                            text    html    latex           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                              text    html    latex   example chm
  spatial                           text    html    latex   example chm
  to.flag                           text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\MANOR~1.RCH\00_PKG~1\MANOR\chm\MANOR.chm


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


Created e:\biocbld\BBS-2~1.4-B\meat\MANOR~1.RCH\00_PKG~1\MANOR\chm\MANOR.chm, 50,430 bytes
Compression decreased file by 63,068 bytes.
** building package indices ...
** MD5 sums
* DONE (MANOR)