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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:rGREAT.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings rGREAT_2.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rGREAT.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
* checking for file ‘rGREAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGREAT’ version ‘2.3.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'BioMartGOGeneSets', 'UniProtKeywords'
* 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 ‘rGREAT’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 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
submitGreatJob 0.396  0.032   9.802
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘local-GREAT.Rmd’ using ‘UTF-8’... OK
  ‘online-GREAT.Rmd’ using ‘UTF-8’... OK
  ‘other-docs.Rmd’ using ‘UTF-8’... OK
  ‘other-geneset-databases.Rmd’ using ‘UTF-8’... OK
  ‘other-organisms.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘local-GREAT.Rmd’ using rmarkdown
--- finished re-building ‘local-GREAT.Rmd’

--- re-building ‘online-GREAT.Rmd’ using rmarkdown
--- finished re-building ‘online-GREAT.Rmd’

--- re-building ‘other-docs.Rmd’ using rmarkdown
--- finished re-building ‘other-docs.Rmd’

--- re-building ‘other-geneset-databases.Rmd’ using rmarkdown
--- finished re-building ‘other-geneset-databases.Rmd’

--- re-building ‘other-organisms.Rmd’ using rmarkdown
trying URL 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_011762595.1/download?include_annotation_type=GENOME_GFF,SEQUENCE_REPORT&filename=GCF_011762595.1.zip'
downloaded 16.2 MB


Quitting from lines 118-120 [unnamed-chunk-10] (other-organisms.Rmd)
Error: processing vignette 'other-organisms.Rmd' failed with diagnostics:
download from 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_011762595.1/download?include_annotation_type=GENOME_GFF,SEQUENCE_REPORT&filename=GCF_011762595.1.zip' failed
--- failed re-building ‘other-organisms.Rmd’

SUMMARY: processing the following file failed:
  ‘other-organisms.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/rGREAT.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL rGREAT
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘rGREAT’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c reduce_by_start_and_end.cpp -o reduce_by_start_and_end.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o rGREAT.so RcppExports.o reduce_by_start_and_end.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-rGREAT/00new/rGREAT/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 (rGREAT)

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)
> suppressWarnings(suppressPackageStartupMessages(library(rGREAT)))
> 
> test_check("rGREAT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 18.803   1.433  20.268