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Package 458/462HostnameOS / ArchBUILDCHECKBUILD BIN
XDE 1.99.0
Robert Scharpf
Snapshot Date: 2011-05-10 07:21:10 -0700 (Tue, 10 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/XDE
Last Changed Rev: 55381 / Revision: 55381
Last Changed Date: 2011-05-10 06:48:51 -0700 (Tue, 10 May 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: XDE
Version: 1.99.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch XDE_1.99.0.tar.gz
StartedAt: 2011-05-10 17:32:07 -0700 (Tue, 10 May 2011)
EndedAt: 2011-05-10 17:34:38 -0700 (Tue, 10 May 2011)
EllapsedTime: 150.6 seconds
RetCode: 0
Status:  OK 
CheckDir: XDE.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/XDE.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘1.99.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘XDE’ 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 ... NOTE
computeGOF: no visible binding for global variable ‘psi’
* checking Rd files ... NOTE
prepare_Rd: firstMcmc.Rd:14-15: Dropping empty section \details
prepare_Rd: thin.Rd:31-32: Dropping empty section \examples
* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘coda’
* 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 compilation flags in Makevars ... 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 ‘XDE.pdf’ from 325Kb to 171Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

XDE.Rcheck/00install.out:

* installing *source* package ‘XDE’ ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Cholesky.cpp -o Cholesky.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Matrix.cpp -o Matrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Random.cpp -o Random.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/usr/include/c++/4.0.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Versions/2.14/Resources/include/R.h:38,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Versions/2.14/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c main.cpp -o main.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o XDE.so Cholesky.o Matrix.o Random.o Structure.o diffExpressed_main.o main.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/XDE.Rcheck/XDE/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Creating a new generic function for "pairs" in "XDE"
Creating a new generic function for "lapply" in "XDE"
Creating a new generic function for "nrow" in "XDE"
Creating a new generic function for "plot" in "XDE"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘XDE.Rnw’ 
   ‘XdeParameterClass.Rnw’ 
** testing if installed package can be loaded

* DONE (XDE)

XDE.Rcheck/XDE-Ex.timings:

nameusersystemelapsed
ExpressionSetList-class0.0470.0040.051
XdeMcmc-class0.0010.0000.001
XdeParameter-class0.0030.0010.004
burnin0.0000.0010.001
empiricalStart0.5380.0120.558
expressionSetList0.0220.0010.024
firstMcmc0.3930.0040.402
geneCenter0.1500.0030.153
hyperparameters0.3720.0030.379
lastMcmc000
output0.2300.0070.241
ssStatistic2.1360.0562.198
studyCenter0.1440.0020.146
symbolsInteresting0.4830.0110.501
xde000
xmcmc0.5350.0270.624
xsScores0.0670.0040.071