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Package 129/251HostnameOS / ArchBUILDCHECKBUILD BIN
maigesPack 1.3.3
Gustavo H. Esteves
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maigesPack
Last Changed Rev: 28882 / Revision: 29143
Last Changed Date: 2007-11-21 10:01:47 -0800 (Wed, 21 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  ERROR 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ ERROR ] OK 
lemming Windows Server 2003 (32-bit) / x64  OK  ERROR  OK 
Package: maigesPack
Version: 1.3.3
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check maigesPack_1.3.3.tar.gz
StartedAt: 2007-12-11 05:10:26 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:15:03 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 277.0 seconds
RetCode: 1
Status: ERROR
CheckDir: maigesPack.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/maigesPack.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-14 r43455)
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.3.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maigesPack' 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 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 maigesPack-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'maigesPack-Ex.R' failed.
The error most likely occurred in:

> ### * normScaleLimma
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: normScaleLimma
> ### Title: Scale adjust a cDNA Microarray Object
> ### Aliases: normScaleLimma
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Doing the scale adjustment from median-absolute-value method (from
> ## limma)
> gastro.norm = normScaleLimma(gastro.norm, method="scale")
> boxplot(gastro.norm) ## To see the efect of adjustment
> 
> ## To do VSN scale adjustment (from vsn package) use the command. Be
> ## carefull that this method adjust the variance along A values and not
> ## between chips!!
> gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
Loading required package: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Warning: The function 'vsn' is deprecated.
It will stay around for some time, for backward compatibility.
For new projects, please use 'vsn2'.
Error in ncol(y@exprs) : 
  no slot of name "exprs" for this object of class "ExpressionSet"
Calls: normScaleLimma -> normalizeBetweenArrays -> ncol
Execution halted

maigesPack.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/maigesPack.Rcheck


---------- Making package maigesPack ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making Minfo.d from Minfo.c
making bootstrapT.d from bootstrapT.c
making register.d from register.c
making robustCorr.d from robustCorr.c
making stats.d from stats.c
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c Minfo.c -o Minfo.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c bootstrapT.c -o bootstrapT.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c register.c -o register.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c robustCorr.c -o robustCorr.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c stats.c -o stats.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i maigesPack_res.rc -o maigesPack_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o maigesPack.dll maigesPack.def Minfo.o bootstrapT.o register.o robustCorr.o stats.o maigesPack_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package maigesPack for lazy loading
Loading required package: convert
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: limma
Loading required package: marray
Loading required package: graph
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'maigesPack'
     Formats: text html latex example chm 
  MI                                text    html    latex   example chm
  activeMod                         text    html    latex   example chm
  activeModScoreHTML                text    html    latex   example chm
  activeNet                         text    html    latex   example chm
  activeNetScoreHTML                text    html    latex   example chm
  addGeneGrps                       text    html    latex   example chm
  addPaths                          text    html    latex   example chm
  bootstrapCor                      text    html    latex   example chm
  bootstrapMI                       text    html    latex   example chm
  bootstrapT                        text    html    latex   example chm
  boxplot-methods                   text    html    latex   example chm
  bracketMethods                    text    html    latex   example chm
  calcA                             text    html    latex   example chm
  calcW                             text    html    latex   example chm
  classifyKNN                       text    html    latex   example chm
  classifyKNNsc                     text    html    latex   example chm
  classifyLDA                       text    html    latex   example chm
  classifyLDAsc                     text    html    latex   example chm
  classifySVM                       text    html    latex   example chm
  classifySVMsc                     text    html    latex   example chm
  coerce-methods                    text    html    latex   example chm
  compCorr                          text    html    latex   example chm
  contrastsFitM                     text    html    latex           chm
  createMaigesRaw                   text    html    latex   example chm
  createTDMS                        text    html    latex           chm
  deGenes2by2BootT                  text    html    latex   example chm
  deGenes2by2Ttest                  text    html    latex   example chm
  deGenes2by2Wilcox                 text    html    latex   example chm
  deGenesANOVA                      text    html    latex   example chm
  designANOVA                       text    html    latex   example chm
  dim-methods                       text    html    latex   example chm
  gastro                            text    html    latex           chm
  getLabels                         text    html    latex   example chm
  heatmapsM                         text    html    latex           chm
  hierM                             text    html    latex   example chm
  hierMde                           text    html    latex   example chm
  image-methods                     text    html    latex   example chm
  kmeansM                           text    html    latex   example chm
  kmeansMde                         text    html    latex   example chm
  loadData                          text    html    latex   example chm
  maiges-class                      text    html    latex           chm
  maigesANOVA-class                 text    html    latex           chm
  maigesActMod-class                text    html    latex           chm
  maigesActNet-class                text    html    latex           chm
  maigesClass-class                 text    html    latex           chm
  maigesDE-class                    text    html    latex           chm
  maigesDEcluster-class             text    html    latex           chm
  maigesPreRaw-class                text    html    latex           chm
  maigesRaw-class                   text    html    latex           chm
  maigesRelNetB-class               text    html    latex           chm
  maigesRelNetM-class               text    html    latex           chm
  normLoc                           text    html    latex   example chm
  normOLIN                          text    html    latex   example chm
  normRepLoess                      text    html    latex   example chm
  normScaleLimma                    text    html    latex   example chm
  normScaleMarray                   text    html    latex   example chm
  plot-methods                      text    html    latex   example chm
  plotGenePair                      text    html    latex   example chm
  print-methods                     text    html    latex   example chm
  relNet2TGF                        text    html    latex   example chm
  relNetworkB                       text    html    latex   example chm
  relNetworkM                       text    html    latex   example chm
  robustCorr                        text    html    latex   example chm
  selSpots                          text    html    latex   example chm
  show-methods                      text    html    latex   example chm
  somM                              text    html    latex   example chm
  somMde                            text    html    latex   example chm
  summarizeReplicates               text    html    latex   example chm
  summary-methods                   text    html    latex   example chm
  tableClass                        text    html    latex   example chm
  tablesDE                          text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.2-bioc\meat\maigesPack.Rcheck\00_pkg_src\maigesPack\chm\maigesPack.chm


Compile time: 0 minutes, 1 second
72	Topics
777	Local links
17	Internet links
1	Graphic


Created e:\biocbld\bbs-2.2-bioc\meat\maigesPack.Rcheck\00_pkg_src\maigesPack\chm\maigesPack.chm, 121,271 bytes
Compression decreased file by 260,540 bytes.
  adding MD5 sums

* DONE (maigesPack)