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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:EGAD.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings EGAD_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EGAD.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 ‘EGAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EGAD’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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 ‘EGAD’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 39.1Mb
  sub-directories of 1Mb or more:
    data  38.8Mb
* checking package 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘EGAD.Rmd’ ‘EGAD.bib’ ‘figures/figure_GO_comb.png’
  ‘figures/figure_aurocs_comparisons.png’
  ‘figures/figure_benchmark.png’ ‘figures/figure_degree_corr.png’
  ‘figures/figure_indirect.png’ ‘figures/figure_mf.png’
  ‘figures/figure_mf_yeast_human.png’
  ‘figures/figure_nd_yeast_human.png’ ‘figures/figure_nv.png’
  ‘figures/figure_nv_yeast_human.png’ ‘figures/figure_overlay.png’
  ‘figures/figure_pheno_comb.png’
  ‘figures/figure_pheno_degree_corr.png’ ‘figures/figure_pheno_mf.png’
  ‘figures/figure_pheno_nv.png’ ‘figures/figure_smoother.png’
  ‘figures/gba_schematic_resized.png’ ‘figures/labels_resized.png’
  ‘figures/mf_schematic.png’ ‘figures/network_resized.png’
  ‘figures/overview_resized.png’
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

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

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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL EGAD
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘EGAD’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (EGAD)