Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 905/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRENITS 1.58.0 (landing page) Edward Morrissey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GRENITS package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GRENITS |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRENITS_1.58.0.tar.gz |
StartedAt: 2024-12-20 21:32:09 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 21:36:05 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 235.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRENITS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRENITS_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GRENITS.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRENITS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GRENITS’ version ‘1.58.0’ * 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 * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 code 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s user system elapsed function_NonLinearNet 102.353 0.318 102.775 function_ReplicatesNet_student 38.621 0.227 38.862 function_ReplicatesNet_gauss 23.534 0.193 23.951 function_LinearNet 14.233 0.092 14.344 analyse.output 13.469 0.110 13.596 readChains 6.145 0.049 6.229 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/GRENITS.Rcheck/00check.log’ for details.
GRENITS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRENITS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GRENITS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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; ^ 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; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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; ^ 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; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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; ^ 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; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_C_interface.cpp -o R_C_interface.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c commonFunctions.cc -o commonFunctions.o 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: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; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c functionsErrorModel.cc -o functionsErrorModel.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o 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: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; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 | 13.469 | 0.110 | 13.596 | |
defaultParams_gauss | 0.011 | 0.001 | 0.013 | |
defaultParams_linear | 0.021 | 0.002 | 0.022 | |
defaultParams_nonLinear | 0.090 | 0.003 | 0.092 | |
defaultParams_student | 0.050 | 0.002 | 0.052 | |
function_LinearNet | 14.233 | 0.092 | 14.344 | |
function_NonLinearNet | 102.353 | 0.318 | 102.775 | |
function_ReplicatesNet_gauss | 23.534 | 0.193 | 23.951 | |
function_ReplicatesNet_student | 38.621 | 0.227 | 38.862 | |
plotPriors | 0.104 | 0.002 | 0.107 | |
readChains | 6.145 | 0.049 | 6.229 | |