Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:49:05 -0400 (Wed, 16 Oct 2019).
Package 717/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GRENITS 1.36.0 Edward Morrissey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: GRENITS |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRENITS_1.36.0.tar.gz |
StartedAt: 2019-10-16 03:28:12 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:33:05 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 292.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRENITS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRENITS_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GRENITS.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.36.0’ * 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 ... OK * checking package directory ... OK * checking ‘build’ 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * 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 global function definition for ‘ggplot’ .heatMap.ggplot: no visible global function definition for ‘aes’ .heatMap.ggplot: no visible binding for global variable ‘Var2’ .heatMap.ggplot: no visible binding for global variable ‘Var1’ .heatMap.ggplot: no visible global function definition for ‘geom_tile’ .heatMap.ggplot: no visible binding for global variable ‘value’ .heatMap.ggplot: no visible global function definition for ‘scale_fill_gradient’ .heatMap.ggplot: no visible global function definition for ‘theme’ .heatMap.ggplot: no visible global function definition for ‘element_blank’ .heatMap.ggplot: no visible global function definition for ‘element_text’ .heatMap.ggplot: no visible global function definition for ‘ggtitle’ .heatMap.ggplot: no visible global function definition for ‘labs’ .heatMap.ggplot: no visible global function definition for ‘scale_x_discrete’ .heatMap.ggplot: no visible global function definition for ‘scale_y_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘ggplot’ .plotDistribParents.LargeMat: no visible global function definition for ‘aes’ .plotDistribParents.LargeMat: no visible binding for global variable ‘variable’ .plotDistribParents.LargeMat: no visible binding for global variable ‘GeneNames’ .plotDistribParents.LargeMat: no visible global function definition for ‘geom_tile’ .plotDistribParents.LargeMat: no visible binding for global variable ‘value’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_fill_gradient’ .plotDistribParents.LargeMat: no visible global function definition for ‘theme’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_blank’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_text’ .plotDistribParents.LargeMat: no visible global function definition for ‘ggtitle’ .plotDistribParents.LargeMat: no visible global function definition for ‘labs’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_x_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_y_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘facet_wrap’ Undefined global functions or variables: GeneNames Var1 Var2 aes element_blank element_text facet_wrap geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete scale_y_discrete theme value variable * 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 compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed function_NonLinearNet 103.250 0.305 104.007 function_ReplicatesNet_student 43.869 0.343 44.318 function_ReplicatesNet_gauss 34.587 0.297 34.898 analyse.output 19.454 0.243 19.887 function_LinearNet 18.616 0.164 19.138 readChains 9.095 0.117 12.052 * 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 vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/GRENITS.Rcheck/00check.log’ for details.
GRENITS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GRENITS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘GRENITS’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c AR1_Student_biocond.cc -o AR1_Student_biocond.o AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c AR1_biocond.cc -o AR1_biocond.o AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c PSplines_biocond.cc -o PSplines_biocond.o PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas; ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_C_interface.cpp -o R_C_interface.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c commonFunctions.cc -o commonFunctions.o commonFunctions.cc:438:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^ commonFunctions.cc:480:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^ 2 warnings generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c functionsErrorModel.cc -o functionsErrorModel.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c updateFunctions_AR1.cc -o updateFunctions_AR1.o updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^ 1 warning generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -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/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-GRENITS/00new/GRENITS/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GRENITS)
GRENITS.Rcheck/GRENITS-Ex.timings
name | user | system | elapsed | |
analyse.output | 19.454 | 0.243 | 19.887 | |
defaultParams_gauss | 0.016 | 0.002 | 0.018 | |
defaultParams_linear | 0.018 | 0.002 | 0.021 | |
defaultParams_nonLinear | 0.135 | 0.007 | 0.142 | |
defaultParams_student | 0.045 | 0.003 | 0.048 | |
function_LinearNet | 18.616 | 0.164 | 19.138 | |
function_NonLinearNet | 103.250 | 0.305 | 104.007 | |
function_ReplicatesNet_gauss | 34.587 | 0.297 | 34.898 | |
function_ReplicatesNet_student | 43.869 | 0.343 | 44.318 | |
plotPriors | 0.158 | 0.004 | 0.162 | |
readChains | 9.095 | 0.117 | 12.052 | |