Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 249/444HostnameOS / ArchBUILDCHECKBUILD BIN
maigesPack 1.15.0
Gustavo H. Esteves
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maigesPack
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ ERROR ] OK 

Summary

Package: maigesPack
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.15.0.tar.gz
StartedAt: 2011-03-17 16:46:22 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 16:53:28 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 425.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: maigesPack.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.15.0'
* 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 installed package size ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... ERROR
Running examples in 'maigesPack-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Method plot for objects defined in this package
> ### Aliases: plot.maigesRaw plot.maiges plot.maigesANOVA plot.maigesDE
> ###   plot.maigesDEcluster plot.maigesClass plot.maigesRelNetB
> ###   plot.maigesRelNetM plot.maigesActMod plot.maigesActNet plot
> ### Keywords: array
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Example with an object of class maigesRaw, without and with backgound
> ## subtraction, also we present a plot with normexp (from limma package)
> ## subtract algorithm.
> plot(gastro.raw[,1], bkgSub="none")
> plot(gastro.raw[,1], bkgSub="subtract")
> plot(gastro.raw[,1], bkgSub="normexp")
Array 1 corrected
Array 1 corrected
> 
> ## Example with an object of class maigesNorm.
> plot(gastro.norm[,1])
> 
> 
> 
> ## Example for objects of class maigesDE.
> 
> ## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
> ## specifies one thousand bootstraps
> gastro.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")
> 
> plot(gastro.ttest) ## Volcano plot
> 
> 
> ## Example for object of class maigesClass.
> 
> ## Doing LDA classifier with 3 genes for the 6th gene group comparing
> ## the 2 categories from 'Type' sample label.
> gastro.class = classifyLDA(gastro.summ, sLabelID="Type",
+   gNameID="GeneName", nGenes=3, geneGrp=6)
> 
> plot(gastro.class) ## plot the 1st classifier
Loading required package: rgl
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
Error in rgl.open() : rgl.open failed
Calls: plot -> plot.maigesClass -> <Anonymous> -> rgl.open
Execution halted

maigesPack.Rcheck/00install.out:

* installing *source* package 'maigesPack' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Minfo.c -o Minfo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c bootstrapT.c -o bootstrapT.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register.c -o register.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c robustCorr.c -o robustCorr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c stats.c -o stats.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck/maigesPack/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: limma
Loading required package: marray
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (maigesPack)

maigesPack.Rcheck/maigesPack-Ex.timings:

nameusersystemelapsed
MI0.0050.0010.004
activeMod3.9330.0123.945
activeModScoreHTML1.9130.0191.932
activeNet5.8410.0045.846
activeNetScoreHTML5.8930.0115.904
addGeneGrps000
addPaths000
bootstrapCor0.0720.0010.074
bootstrapMI0.2960.0010.297
bootstrapT0.0050.0010.005
boxplot-methods112.238 2.477114.719
bracketMethods0.3070.0110.318
calcA0.2720.1400.412
calcW0.2680.1360.405
classifyKNN0.3560.0060.363
classifyKNNsc0.5000.0030.503
classifyLDA1.7410.0081.749
classifyLDAsc2.9640.0042.968
classifySVM0.8020.0050.808
classifySVMsc1.3520.0031.355
coerce-methods0.2120.0250.236
compCorr000
createMaigesRaw0.4780.0050.483
deGenes2by2BootT0.9410.0060.947
deGenes2by2Ttest0.4360.0030.437
deGenes2by2Wilcox0.3940.0030.396
deGenesANOVA0.4170.0050.422
designANOVA0.1710.0040.175
dim-methods0.1070.0010.108
getLabels0.1140.0070.120
hierM2.6110.0782.635
hierMde0.6310.0110.641
image-methods4.4450.3394.784
kmeansM2.4080.0622.454
kmeansMde0.6120.0090.632
loadData000
normLoc2.7780.0862.864
normOLIN0.1130.0020.115
normRepLoess0.1140.0020.116
normScaleLimma103.658 1.741105.613
normScaleMarray71.832 0.22372.057