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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings FELLA_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FELLA.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 ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.21.0’
* package encoding: UTF-8
* 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 ‘FELLA’ can be installed ... OK
* 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 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 ... NOTE
buildGraphFromKEGGREST: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
enrich-funs 3.632  1.036   5.958
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 3923885 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘musmusculus.Rmd’ using ‘UTF-8’... OK
  ‘quickstart.Rmd’ using ‘UTF-8’... OK
  ‘zebrafish.Rmd’ using ‘UTF-8’... OK
  ‘FELLA.Rnw’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘FELLA.Rnw’
  ...
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Directory /home/biocbuild/tmp/RtmpJFJGtx/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘musmusculus.Rmd’ using rmarkdown

Quitting from lines 75-84 [unnamed-chunk-2] (musmusculus.Rmd)
Error: processing vignette 'musmusculus.Rmd' failed with diagnostics:
Timeout was reached: [rest.kegg.jp] Connection timeout after 10001 ms
--- failed re-building ‘musmusculus.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png" but not available.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘zebrafish.Rmd’ using rmarkdown
Warning: LaTeX Warning: You have requested package `/home/biocbuild/R/R-4.3.1/site-libra
Warning: ry/BiocStyle/resources/tex/Bioconductor',
Warning:                but the package provides `Bioconductor'.
--- finished re-building ‘zebrafish.Rmd’

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid
Done.
Building graph...
Filtering 5 pathways.
Done.
Pruning graph...
Current weight: 1 out of 4...
Current weight: 2 out of 4...
Current weight: 3 out of 4...
Current weight: 4 out of 4...
Done.
Computing probabilities for random subgraphs... (this may take a while)
Directory /home/biocbuild/tmp/Rtmp3ZUgC1/my_database does not exist. Creating it...
Done.
Done.
Computing diffusion.matrix... (this may take a while and use some memory)
SUMMARY: processing the following files failed:
  ‘musmusculus.Rmd’ ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL FELLA
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘FELLA’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FELLA)

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(FELLA)
> 
> test_check("FELLA")

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