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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Category.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Category_2.66.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Category.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.66.0’
* 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 ‘Category’ 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 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) cb_parse_band_Hs.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cb_parse_band_Mm.Rd:22: Escaped LaTeX specials: \&
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘KEGG.db’ in Rd xrefs
* 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 ‘Category-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPathNames
> ### Title: A function to print pathway names given their numeric ID.
> ### Aliases: getPathNames
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
>  nms = "00031"
>  getPathNames(nms) 
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Forbidden (HTTP 403).
Calls: getPathNames -> <Anonymous> -> .getUrl -> stop_for_status
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Category.Rnw’... failed
  ‘ChromBand.Rnw’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘Category.Rnw’
  ...

> byTT = names(tA)[tA < -7]

> KEGGmnplot(byTT, eS, group = eS$mol, data = "hgu95av2", 
+     main = paste(getPathNames(byTT)[[1]], paste("Overall:", round(tA[byTT], 
+         3) .... [TRUNCATED] 

  When sourcing ‘Category.R’:
Error: Forbidden (HTTP 403).
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘Category.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: XML
Loading required package: org.Hs.eg.db


Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand


Error: processing vignette 'Category.Rnw' failed with diagnostics:
 chunk 10 (label = KEGGmnplot) 
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Forbidden (HTTP 403).

--- failed re-building ‘Category.Rnw’

--- re-building ‘ChromBand.Rnw’ using Sweave
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Loading required package: org.Hs.eg.db


Loading required package: XML
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: lattice

Attaching package: 'limma'

The following object is masked from 'package:geneplotter':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA


Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

--- finished re-building 'ChromBand.Rnw'

SUMMARY: processing the following file failed:
  ‘Category.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Category.Rcheck/00check.log’
for details.