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 282/631HostnameOS / ArchBUILDCHECKBUILD BIN
GRENITS 1.11.0
Edward Morrissey
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRENITS
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / 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 

Summary

Package: GRENITS
Version: 1.11.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GRENITS_1.11.0.tar.gz
StartedAt: 2013-01-16 03:22:04 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:26:54 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 290.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.11.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GRENITS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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/biocbuild/bbs-2.12-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
Examples with CPU or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          84.597  0.064  84.685
function_ReplicatesNet_student 36.938  0.212  37.152
function_ReplicatesNet_gauss   24.678  0.172  24.850
analyse.output                 11.280  0.056  11.396
function_LinearNet             10.905  0.084  10.993
readChains                      5.777  0.044   5.819
* 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/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

GRENITS.Rcheck/00install.out:

* installing *source* package ‘GRENITS’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c AR1_biocond.cc -o AR1_biocond.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c PSplines_biocond.cc -o PSplines_biocond.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c R_C_interface.cpp -o R_C_interface.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-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
/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:329:1: 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*)’
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -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 ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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)

GRENITS.Rcheck/GRENITS-Ex.timings:

nameusersystemelapsed
analyse.output11.280 0.05611.396
defaultParams_gauss0.0440.0000.044
defaultParams_linear0.0520.0000.051
defaultParams_nonLinear0.3280.0080.335
defaultParams_student0.0760.0000.077
function_LinearNet10.905 0.08410.993
function_NonLinearNet84.597 0.06484.685
function_ReplicatesNet_gauss24.678 0.17224.850
function_ReplicatesNet_student36.938 0.21237.152
plotPriors0.2240.0040.228
readChains5.7770.0445.819