XDE 2.2.0
Robert Scharpf
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/XDE | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/XDE.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XDE/DESCRIPTION' ... OK
* this is package 'XDE' version '2.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'XDE' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 4.5Mb
* 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 ... 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/XDE.Rcheck/XDE/libs/XDE.so':
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Objects: 'Cholesky.o', 'Random_v2.o', 'Structure.o', 'Update_v2.o',
'diffExpressed_main.o'
Found 'exit', possibly from 'exit' (C)
Objects: 'Cholesky.o', 'Random_v2.o', 'Structure.o', 'Update_v2.o',
'Utility_v2.o', 'diffExpressed_main.o'
Found 'stderr', possibly from 'stderr' (C)
Object: 'Utility_v2.o'
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... 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
NOTE: There were 3 notes.
See
'/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/XDE.Rcheck/00check.log'
for details.
* installing *source* package 'XDE' ...
** libs
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Cholesky.cpp -o Cholesky.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Potential_v2.cpp -o Potential_v2.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Random_v2.cpp -o Random_v2.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8:0,
from Rinterface_v2.cpp:3:
Random.h:19:0: warning: "PI" redefined [enabled by default]
/home/hpages/test-puck5/bbs-2.10-bioc/R/include/R_ext/Constants.h:30:0: note: this is the location of the previous definition
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.6/backward/strstream:52:0,
from Structure.cpp:1:
/usr/include/c++/4.6/backward/backward_warning.h:33:2: 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. [-Wcpp]
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Update_v2.cpp -o Update_v2.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Utility_v2.cpp -o Utility_v2.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -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 [enabled by default]
/home/hpages/test-puck5/bbs-2.10-bioc/R/include/R_ext/Constants.h:30:0: note: this is the location of the previous definition
g++ -shared -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'pairs' from package 'graphics' in package 'XDE'
Creating a generic function for 'plot' from package 'graphics' in package 'XDE'
** help
*** installing help indices
** building package indices
** installing vignettes
'XDE.Rnw'
'XdeParameterClass.Rnw'
** testing if installed package can be loaded
* DONE (XDE)