XDE 1.12.0
Robert Scharpf
| 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/XDE | | Last Changed Rev: 54808 / Revision: 59457 | | Last Changed Date: 2011-04-13 18:03:42 -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 | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/XDE.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘1.12.0’
* checking package namespace 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 ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
libs 5.4Mb
data 1.9Mb
* 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 ... 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 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
* installing *source* package ‘XDE’ ...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Cholesky.cpp -o Cholesky.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Matrix.cpp -o Matrix.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Random.cpp -o Random.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.5/backward/strstream:47:0,
from Structure.cpp:1:
/usr/include/c++/4.5/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:0:
Random.h:19:0: warning: "PI" redefined
/home/biocbuild/bbs-2.8-bioc/R/include/R_ext/Constants.h:30:0: note: this is the location of the previous definition
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -c main.cpp -o main.o
g++ -shared -L/usr/local/lib64 -o XDE.so Cholesky.o Matrix.o Random.o Structure.o diffExpressed_main.o main.o -lm -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
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 ...
** testing if installed package can be loaded
* DONE (XDE)