Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 218/479HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: GRENITS
Version: 1.4.1
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GRENITS_1.4.1.tar.gz
StartedAt: 2011-07-07 04:34:49 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:40:44 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 355.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GRENITS.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (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 '1.4.1'
* 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 ... OK
* checking package directory ... OK
* checking for portable file names ... 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

GRENITS.Rcheck/00install.out:

* installing *source* package 'GRENITS' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c AR1_biocond.cc -o AR1_biocond.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c PSplines_biocond.cc -o PSplines_biocond.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c R_C_interface.cpp -o R_C_interface.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -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
D:/biocbld/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
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c functionsErrorModel.cc -o functionsErrorModel.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -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
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o GRENITS.dll tmp.def 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 D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/lib/x64/libRcpp.a -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRblas -lgfortran -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GRENITS.Rcheck/GRENITS/libs/x64
** 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)

GRENITS.Rcheck/GRENITS-Ex.timings:

nameusersystemelapsed
analyse.output18.98 0.1019.36
defaultParams_gauss0.010.000.02
defaultParams_linear0.020.000.02
defaultParams_nonLinear0.280.000.28
defaultParams_student0.010.000.01
function_LinearNet18.50 0.0918.82
function_NonLinearNet106.23 0.06106.58
function_ReplicatesNet_gauss40.82 0.1341.23
function_ReplicatesNet_student56.11 0.2256.37
plotPriors0.260.000.27
readChains7.710.057.76