GRENITS 1.8.0
Edward Morrissey
| 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/GRENITS | | 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/GRENITS.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 'GRENITS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GRENITS' version '1.8.0'
* 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 'GRENITS' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 5.9Mb
* 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
.heatMap.ggplot: no visible binding for global variable 'Var2'
.heatMap.ggplot: no visible binding for global variable 'Var1'
.heatMap.ggplot: no visible binding for global variable 'value'
.plotDistribParents.LargeMat: no visible binding for global variable
'variable'
.plotDistribParents.LargeMat: no visible binding for global variable
'GeneNames'
.plotDistribParents.LargeMat: no visible binding for global variable
'value'
* 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/GRENITS.Rcheck/GRENITS/libs/GRENITS.so':
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Object: 'commonFunctions.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/GRENITS.Rcheck/00check.log'
for details.
* installing *source* package 'GRENITS' ...
** libs
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c AR1_biocond.cc -o AR1_biocond.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c PSplines_biocond.cc -o PSplines_biocond.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c R_C_interface.cpp -o R_C_interface.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:22:66: warning: declaration of 'void dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' with C language linkage [enabled by default]
/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:290:1: warning: conflicts with previous declaration 'void arma::dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, const double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' [enabled by default]
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
g++ -shared -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Rcpp/lib -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRlapack -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/GRENITS.Rcheck/GRENITS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GRENITS_package.Rnw'
** testing if installed package can be loaded
* DONE (GRENITS)