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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings PPInfer_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/PPInfer.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘PPInfer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PPInfer’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'biomaRt', 'fgsea', 'kernlab', 'ggplot2', 'igraph', 'STRINGdb',
  'yeastExpData'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PPInfer’ 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 ... 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 sizes of PDF files under ‘inst/doc’ ...* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PPInfer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ppi.infer.human
> ### Title: Inferring functionally related proteins using protein networks
> ###   for human
> ### Aliases: ppi.infer.human
> 
> ### ** Examples
> 
> # example 1
> string.db.9606 <- STRINGdb$new(version = '11', species = 9606,
+                                score_threshold = 999)
> string.db.9606.graph <- string.db.9606$get_graph()
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 71241372 bytes (67.9 MB)
=================================================
downloaded 66.8 MB

Warning in download.file(urlStr, temp) :
  downloaded length 70008570 != reported length 71241372
Warning in download.file(urlStr, temp) :
  URL 'https://stringdb-downloads.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz': Timeout of 600 seconds was reached
Error in download.file(urlStr, temp) : 
  download from 'https://stringdb-downloads.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz' failed
Calls: <Anonymous> -> load -> downloadAbsentFile -> download.file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ORA.barplot 2.119  0.086  16.579
ORA         1.700  0.133  16.207
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/PPInfer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL PPInfer
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘PPInfer’ ...
** this is package ‘PPInfer’ version ‘1.37.0’
** 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 (PPInfer)