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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CoSIA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CoSIA_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CoSIA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CoSIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoSIA’ version ‘1.10.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
 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 ‘CoSIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CoSIA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCVGEx
> ### Title: plotCVGEx Generic
> ### Aliases: plotCVGEx
> 
> ### ** Examples
> 
> Kidney_Genes <- CoSIAn(
+     gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
+     i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
+         "h_sapiens", "r_norvegicus"
+     ), output_ids = c("Ensembl_id", "Symbol"),
+     mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
+     map_tissues = c("adult mammalian kidney","heart"), 
+     map_species = c("h_sapiens", "r_norvegicus"),
+     metric_type = "CV_Tissue"
+ )
> Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
'select()' returned 1:1 mapping between keys and columns
Joining with `by = join_by(h_sapiens_ensembl_id)`
Joining with `by = join_by(h_sapiens_ensembl_id)`
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Joining with `by = join_by(h_sapiens_ensembl_id)`
Joining with `by = join_by(h_sapiens_ensembl_id)`
> Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
CoSIAdata not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: getGExMetrics ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
plotCVGEx-CoSIAn-method     157.131  3.339 161.197
getTissues                   56.405  1.060  57.738
getGEx-CoSIAn-method         11.561  0.342  12.509
getGExMetrics-CoSIAn-method  11.606  0.239  12.116
getGEx                       11.175  0.239  11.690
getGExMetrics                11.028  0.190  11.493
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘CoSIA_Intro.Rmd’ using rmarkdown

Quitting from CoSIA_Intro.Rmd:103-105 [getTissues_2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─CoSIA::getTissues(c("m_musculus", "r_norvegicus"))
 2.   └─base::lapply(species, CoSIAdata_load)
 3.     └─CoSIA (local) FUN(X[[i]], ...)
 4.       └─ExperimentHub::ExperimentHub()
 5.         └─AnnotationHub::.Hub(...)
 6.           └─base::tryCatch(...)
 7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.                 └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CoSIA_Intro.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘CoSIA_Intro.Rmd’

SUMMARY: processing the following file failed:
  ‘CoSIA_Intro.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CoSIA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CoSIA
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CoSIA’ ...
** this is package ‘CoSIA’ version ‘1.10.1’
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoSIA)