Edward Morrissey
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/GRENITS |
| git_branch: RELEASE_3_18 |
| git_last_commit: 15861aa |
| git_last_commit_date: 2023-10-24 09:47:18 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:22 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 902/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRENITS 1.54.0 (landing page) Edward Morrissey
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the GRENITS package: - 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: 1.54.0 |
| 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_1.54.0.tar.gz |
| StartedAt: 2024-03-27 15:21:20 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:25:08 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 227.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GRENITS.Rcheck |
| Warnings: 0 |
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### 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_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GRENITS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.54.0’
* 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 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 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 89.916 0.201 90.242
function_ReplicatesNet_student 37.860 0.281 38.318
function_ReplicatesNet_gauss 25.681 0.195 26.014
function_LinearNet 14.446 0.086 14.541
analyse.output 13.809 0.108 13.962
readChains 6.108 0.049 6.221
* 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-3.18-bioc-mac-arm64/meat/GRENITS.Rcheck/00check.log’
for details.
GRENITS.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRENITS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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 | 13.809 | 0.108 | 13.962 | |
| defaultParams_gauss | 0.064 | 0.002 | 0.065 | |
| defaultParams_linear | 0.021 | 0.001 | 0.023 | |
| defaultParams_nonLinear | 0.092 | 0.003 | 0.097 | |
| defaultParams_student | 0.050 | 0.002 | 0.053 | |
| function_LinearNet | 14.446 | 0.086 | 14.541 | |
| function_NonLinearNet | 89.916 | 0.201 | 90.242 | |
| function_ReplicatesNet_gauss | 25.681 | 0.195 | 26.014 | |
| function_ReplicatesNet_student | 37.860 | 0.281 | 38.318 | |
| plotPriors | 0.136 | 0.004 | 0.158 | |
| readChains | 6.108 | 0.049 | 6.221 | |