Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GRENITS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRENITS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 810/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRENITS 1.44.0 (landing page) Edward Morrissey
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GRENITS |
Version: 1.44.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRENITS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GRENITS_1.44.0.tar.gz |
StartedAt: 2021-10-15 00:05:28 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:12:32 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 424.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRENITS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRENITS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GRENITS_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GRENITS.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-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 '1.44.0' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GRENITS/libs/i386/GRENITS.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GRENITS/libs/x64/GRENITS.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed function_NonLinearNet 77.69 0.05 80.58 function_ReplicatesNet_student 34.66 0.07 34.89 function_ReplicatesNet_gauss 23.71 0.11 25.26 analyse.output 14.53 0.11 19.77 function_LinearNet 13.71 0.02 14.69 readChains 5.98 0.02 6.00 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed function_NonLinearNet 69.04 0.04 70.20 function_ReplicatesNet_student 35.83 0.12 37.03 function_ReplicatesNet_gauss 19.59 0.07 19.80 analyse.output 12.17 0.11 13.11 function_LinearNet 10.48 0.05 10.53 readChains 7.39 0.03 7.94 * 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GRENITS.Rcheck/00check.log' for details.
GRENITS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GRENITS_1.44.0.tar.gz && rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GRENITS.buildbin-libdir GRENITS_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GRENITS_1.44.0.zip && rm GRENITS_1.44.0.tar.gz GRENITS_1.44.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 66696 100 66696 0 0 421k 0 --:--:-- --:--:-- --:--:-- 422k install for i386 * installing *source* package 'GRENITS' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_Student_biocond.cc -o AR1_Student_biocond.o AR1_Student_biocond.cc: In function 'void Error_Student_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_biocond.cc -o AR1_biocond.o AR1_biocond.cc: In function 'void AR1_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PSplines_biocond.cc -o PSplines_biocond.o PSplines_biocond.cc: In function 'void PSplines_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas; ^~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_C_interface.cpp -o R_C_interface.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c commonFunctions.cc -o commonFunctions.o commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)': commonFunctions.cc:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < seq.n_elem; i++) ~~^~~~~~~~~~~~ commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)': commonFunctions.cc:315:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable] clock_t so_far_clock, time_now; //so_far_sec, ^~~~~~~~~~~~ commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)': commonFunctions.cc:375:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i = 0; i!=Gamma_fixed.n_cols;i++) ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc:378:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j = 0; j!=Gamma_fixed.n_cols;j++) ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)': commonFunctions.cc:438:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)': commonFunctions.cc:480:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c functionsErrorModel.cc -o functionsErrorModel.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updateFunctions_AR1.cc -o updateFunctions_AR1.o updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, const mat&, const double&, const unsigned int&)': updateFunctions_AR1.cc:128:34: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] for(int j_loop = 0; j_loop < genes; j_loop++) ~~~~~~~^~~~~~~ updateFunctions_AR1.cc:134:8: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (i != j) ~~^~~~ updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)': updateFunctions_AR1.cc:186:34: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)': updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updateFunctions_Splines.cc -o updateFunctions_Splines.o updateFunctions_Splines.cc: In function 'void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)': updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void initBasesOn(arma::urowvec&, const umat&, int, int)': updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const mat&, double, double, int, double, double, double, double, int, double, arma::uvec)': updateFunctions_Splines.cc:296:10: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(i == indxReg) ~~^~~~~~~~~~ updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)': updateFunctions_Splines.cc:478:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)': updateFunctions_Splines.cc:714:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(base_k = 0; base_k != M; base_k++) ~~~~~~~^~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GRENITS.buildbin-libdir/00LOCK-GRENITS/00new/GRENITS/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GRENITS' finding HTML links ... done LockeData html LockeDataError html analyse.output html defaultParams_gauss html defaultParams_linear html defaultParams_nonLinear html defaultParams_student html function_LinearNet html function_NonLinearNet html function_ReplicatesNet_gauss html function_ReplicatesNet_student html plotPriors html readChains html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'GRENITS' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_Student_biocond.cc -o AR1_Student_biocond.o AR1_Student_biocond.cc: In function 'void Error_Student_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AR1_biocond.cc -o AR1_biocond.o AR1_biocond.cc: In function 'void AR1_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~~~ AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable] int num_fixedON, numDiag, p_sqr, free_gammas; ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PSplines_biocond.cc -o PSplines_biocond.o PSplines_biocond.cc: In function 'void PSplines_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)': PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable] int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas; ^~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_C_interface.cpp -o R_C_interface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c commonFunctions.cc -o commonFunctions.o commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)': commonFunctions.cc:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < seq.n_elem; i++) ~~^~~~~~~~~~~~ commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)': commonFunctions.cc:315:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable] clock_t so_far_clock, time_now; //so_far_sec, ^~~~~~~~~~~~ commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)': commonFunctions.cc:375:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i = 0; i!=Gamma_fixed.n_cols;i++) ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc:378:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j = 0; j!=Gamma_fixed.n_cols;j++) ~^~~~~~~~~~~~~~~~~~~~ commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)': commonFunctions.cc:438:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)': commonFunctions.cc:480:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c functionsErrorModel.cc -o functionsErrorModel.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updateFunctions_AR1.cc -o updateFunctions_AR1.o updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, const mat&, const double&, const unsigned int&)': updateFunctions_AR1.cc:128:34: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] for(int j_loop = 0; j_loop < genes; j_loop++) ~~~~~~~^~~~~~~ updateFunctions_AR1.cc:134:8: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if (i != j) ~~^~~~ updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)': updateFunctions_AR1.cc:186:34: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)': updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable] unsigned int num_on; ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c updateFunctions_Splines.cc -o updateFunctions_Splines.o updateFunctions_Splines.cc: In function 'void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)': updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void initBasesOn(arma::urowvec&, const umat&, int, int)': updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~~~ updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable] int G, start_indx, end_indx; ^~~~~~~~ updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const mat&, double, double, int, double, double, double, double, int, double, arma::uvec)': updateFunctions_Splines.cc:296:10: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(i == indxReg) ~~^~~~~~~~~~ updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)': updateFunctions_Splines.cc:478:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++) ~~~~~~~^~~~~~~~~~~~~~~~ updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)': updateFunctions_Splines.cc:714:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(base_k = 0; base_k != M; base_k++) ~~~~~~~^~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GRENITS' as GRENITS_1.44.0.zip * DONE (GRENITS) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'GRENITS' successfully unpacked and MD5 sums checked
GRENITS.Rcheck/examples_i386/GRENITS-Ex.timings
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GRENITS.Rcheck/examples_x64/GRENITS-Ex.timings
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