##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mogsa_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.40.0’
* 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 ‘mogsa’ 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 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 ... NOTE
checkRd: (-1) GIS.Rd:57: Lost braces; missing escapes or markup?
    57 |         log2(var(GS_{-i})/var(GS))
       |                     ^
checkRd: (-1) GIS.Rd:59: Lost braces; missing escapes or markup?
    59 |         where GS is the gene set score, and the GS_{-i} is a recalculate of 
       |                                                    ^
checkRd: (-1) GIS.Rd:65: Lost braces; missing escapes or markup?
    65 |         log2(F(GS_{-i})/F(GS))
       |                   ^
checkRd: (-1) NCI60_4array_supdata.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mgsa-class.Rd:22-24: Lost braces
    22 |                 \item{combine}{\code{signature(x = "mgsa", y = "mgsa")}}{
       |                                                                         ^
* 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 ... ERROR
Running examples in ‘mogsa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prepGraphite
> ### Title: Prepare pathway gene sets from graphite package
> ### Aliases: prepGraphite
> ### Keywords: pahtways graphite
> 
> ### ** Examples
> 
>   library(graphite)
>   keggdb <- prepGraphite(db = pathways("hsapiens", "kegg")[1:3], id = "entrez")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?
Calls: prepGraphite -> pathways -> loadData -> fetchRemote
Execution halted
* 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 ‘moCluster-knitr.Rnw’ using knitr
--- finished re-building ‘moCluster-knitr.Rnw’

--- re-building ‘mogsa-knitr.Rnw’ using knitr
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'
Warning: 'mode(width)' differs between new and previous
	 ==> NOT changing 'width'

Quitting from lines 278-282 [prepGraphite] (mogsa-knitr.Rnw)
Error: processing vignette 'mogsa-knitr.Rnw' failed with diagnostics:
cannot download pathway data: are you offline?
--- failed re-building ‘mogsa-knitr.Rnw’

SUMMARY: processing the following file failed:
  ‘mogsa-knitr.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mogsa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘mogsa’ ...
** 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 (mogsa)