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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IsoBayes.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings IsoBayes_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/IsoBayes.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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
* using option ‘--no-vignettes’
* checking for file ‘IsoBayes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoBayes’ version ‘1.0.0’
* 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 ‘IsoBayes’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.2Mb
    libs      2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 ... ERROR
Running examples in ‘IsoBayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_relative_abundances
> ### Title: Plot isoform results
> ### Aliases: plot_relative_abundances
> 
> ### ** Examples
> 
> # Load internal data to the package:
> data_dir = system.file("extdata", package = "IsoBayes")
> 
> # Define the path to the AllPeptides.psmtsv file returned by MetaMorpheus tool
> path_to_peptides_psm = paste0(data_dir, "/AllPeptides.psmtsv")
> 
> # Define the path to the jurkat_isoform_kallisto.tsv with mRNA relative abundance
> tpm_path = paste0(data_dir, "/jurkat_isoform_kallisto.tsv")
> 
> # Load the data
> data_loaded = load_data(
+     path_to_peptides_psm = path_to_peptides_psm,
+     path_to_tpm = tpm_path
+ )
We found:
10647 protein isoforms.
After FDR filtering (if used), we will analyze:
7521 protein isoforms.
Percentage of unique peptides:
46.26%
> 
> # Define the path to the map_iso_gene.csv file
> path_to_map_iso_gene = paste0(data_dir, "/map_iso_gene.csv")
> 
> # Run the algorithm
> set.seed(169612)
> results = inference(data_loaded, map_iso_gene = path_to_map_iso_gene)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1372950 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IsoBayes)
  > test_check("IsoBayes")
* 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: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/IsoBayes.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL IsoBayes
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘IsoBayes’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MCMC.cpp -o MCMC.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MCMC_PEP.cpp -o MCMC_PEP.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MCMC_Unique.cpp -o MCMC_Unique.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o IsoBayes.so MCMC.o MCMC_PEP.o MCMC_Unique.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-IsoBayes/00new/IsoBayes/libs
** R
** 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 (IsoBayes)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(IsoBayes)
> test_check("IsoBayes")