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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PPInfer_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PPInfer.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PPInfer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PPInfer’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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 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
ORA: no visible global function definition for ‘txtProgressBar’
ORA: no visible global function definition for ‘fisher.test’
ORA: no visible global function definition for ‘setTxtProgressBar’
ORA: no visible global function definition for ‘p.adjust’
ORA.barplot: no visible global function definition for ‘p.adjust’
enrich.net: no visible global function definition for ‘stack’
enrich.net: no visible global function definition for ‘adjustcolor’
enrich.net : <anonymous>: no visible global function definition for
  ‘adjustcolor’
enrich.net: no visible binding for global variable ‘legend’
net.infer: no visible global function definition for ‘na.omit’
net.infer.ST: no visible global function definition for ‘na.omit’
ppi.infer.human: no visible global function definition for ‘na.omit’
ppi.infer.mouse: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar
  stack txtProgressBar
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "legend")
  importFrom("stats", "fisher.test", "na.omit", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar")
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 sizes of PDF files under ‘inst/doc’ ... OK
* 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.mouse
> ### Title: Inferring functionally related proteins using protein networks
> ###   for mouse
> ### Aliases: ppi.infer.mouse
> 
> ### ** Examples
> 
> string.db.10090 <- STRINGdb$new(version = '11', species = 10090,
+                                 score_threshold = 999)
> string.db.10090.graph <- string.db.10090$get_graph()
trying URL 'https://stringdb-static.org/download/protein.links.v11.0/10090.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 70223084 bytes (67.0 MB)
==================================================
downloaded 67.0 MB

> K.10090 <- net.kernel(string.db.10090.graph)
> rownames(K.10090) <- substring(rownames(K.10090), 7)
> colnames(K.10090) <- substring(colnames(K.10090), 7)
> target <- colnames(K.10090)[1:100]
> infer.mouse <- ppi.infer.mouse(target, K.10090, input="ensembl_peptide_id")
Error in read_html.response(GET(url)) : Bad Gateway (HTTP 502).
Calls: ppi.infer.mouse ... <Anonymous> -> <Anonymous> -> read_html.response -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/PPInfer.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PPInfer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PPInfer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PPInfer.Rnw’ 
** 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)