GRENITS 1.4.1
Edward Morrissey
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRENITS | | Last Changed Rev: 56559 / Revision: 56603 | | Last Changed Date: 2011-07-05 10:02:03 -0700 (Tue, 05 Jul 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 |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GRENITS.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.4.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GRENITS’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 6.2Mb
* 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
.heatMap.ggplot: no visible binding for global variable ‘X2’
.heatMap.ggplot: no visible binding for global variable ‘X1’
.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 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 ‘GRENITS’ ...
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c AR1_biocond.cc -o AR1_biocond.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c PSplines_biocond.cc -o PSplines_biocond.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c R_C_interface.cpp -o R_C_interface.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -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
/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:296:1: warning: conflicts with previous declaration ‘void arma::lapack::dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, const double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)’
commonFunctions.cc: In function ‘void random_intSequence(arma::ucolvec&)’:
commonFunctions.cc:219:27: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&)’:
updateFunctions_AR1.cc:123:36: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc:129:11: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&, const arma::umat&)’:
updateFunctions_AR1.cc:174:36: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/RcppArmadillo/include" -fpic -g -O2 -Wall -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
g++ -shared -L/usr/local/lib64 -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.9-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/GRENITS.Rcheck/GRENITS/libs
** R
** data
** inst
** preparing package for lazy loading
Loading required package: reshape
Loading required package: plyr
Attaching package: ‘reshape’
The following object(s) are masked from ‘package:plyr’:
rename, round_any
Loading required package: grid
Loading required package: proto
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘GRENITS_package.Rnw’
** testing if installed package can be loaded
* DONE (GRENITS)