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This page was generated on 2023-06-06 11:00:33 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for GRENITS on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 869/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRENITS 1.53.1  (landing page)
Edward Morrissey
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/GRENITS
git_branch: devel
git_last_commit: 25b6174
git_last_commit_date: 2023-05-02 13:46:57 -0000 (Tue, 02 May 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: GRENITS
Version: 1.53.1
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GRENITS_1.53.1.tar.gz
StartedAt: 2023-06-05 23:42:05 -0000 (Mon, 05 Jun 2023)
EndedAt: 2023-06-05 23:46:23 -0000 (Mon, 05 Jun 2023)
EllapsedTime: 258.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings GRENITS_1.53.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GRENITS.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.53.1’
* 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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          82.652  0.044  82.817
function_ReplicatesNet_student 36.322  0.040  36.411
function_ReplicatesNet_gauss   28.484  0.048  28.568
analyse.output                 16.262  0.052  16.335
function_LinearNet             16.171  0.036  16.222
readChains                      7.911  0.032   7.950
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GRENITS_package.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

Installation output

GRENITS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL GRENITS
###
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##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘GRENITS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c AR1_biocond.cc -o AR1_biocond.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c PSplines_biocond.cc -o PSplines_biocond.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c R_C_interface.cpp -o R_C_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c commonFunctions.cc -o commonFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/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 -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-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)

Tests output

Example timings

GRENITS.Rcheck/GRENITS-Ex.timings

nameusersystemelapsed
analyse.output16.262 0.05216.335
defaultParams_gauss0.0160.0040.019
defaultParams_linear0.0150.0000.015
defaultParams_nonLinear0.1120.0040.116
defaultParams_student0.0260.0040.030
function_LinearNet16.171 0.03616.222
function_NonLinearNet82.652 0.04482.817
function_ReplicatesNet_gauss28.484 0.04828.568
function_ReplicatesNet_student36.322 0.04036.411
plotPriors0.1410.0000.141
readChains7.9110.0327.950