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Package 266/467HostnameOS / ArchBUILDCHECKBUILD BIN
maigesPack 1.16.0
Gustavo H. Esteves
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/maigesPack
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
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 SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ ERROR ] OK 

Summary

Package: maigesPack
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.16.0.tar.gz
StartedAt: 2011-10-20 15:47:53 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 16:00:00 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 726.8 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 2.13.2 (2011-09-30)
* 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 '1.16.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'maigesPack_tutorial.pdf' from 386Kb to 189Kb
  consider running tools::compactPDF() on these files
* 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-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (maigesPack)

maigesPack.Rcheck/maigesPack-Ex.timings:

nameusersystemelapsed
MI0.0140.0000.015
activeMod4.9540.0545.339
activeModScoreHTML2.5350.0522.948
activeNet7.6220.0347.875
activeNetScoreHTML7.6140.0367.716
addGeneGrps0.0010.0010.002
addPaths000
bootstrapCor0.0900.0010.095
bootstrapMI0.4230.0050.430
bootstrapT0.0050.0000.005
boxplot-methods150.157 46.831206.175
bracketMethods0.5130.0600.656
calcA0.3420.2240.587
calcW0.3550.2400.671
classifyKNN0.4820.0190.524
classifyKNNsc0.6700.0150.691
classifyLDA2.2710.0292.618
classifyLDAsc3.8670.0244.121
classifySVM1.0570.0181.102
classifySVMsc1.7560.0181.818
coerce-methods0.2840.0680.352
compCorr000
createMaigesRaw0.6030.0160.621
deGenes2by2BootT1.2400.0141.257
deGenes2by2Ttest0.6420.0140.663
deGenes2by2Wilcox0.5130.0110.526
deGenesANOVA0.5360.0330.572
designANOVA0.2400.0180.258
dim-methods0.1590.0060.165
getLabels0.1660.0170.183
hierM3.3910.2043.617
hierMde0.8260.0240.909
image-methods 7.182 3.60711.104
kmeansM3.1630.1973.408
kmeansMde0.7760.0180.805
loadData0.0000.0010.001
normLoc4.6540.4695.162
normOLIN0.1590.0060.165
normRepLoess0.1590.0060.165
normScaleLimma178.039 34.709219.428
normScaleMarray 84.603 17.074110.125