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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings topGO_2.51.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.51.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi',
  'SparseM'
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 ‘topGO’ can be installed ... 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 ... WARNING
Error in library(topGO, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘topGO’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘Rgraphviz’ ‘multtest’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘globaltest:::globaltest’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOplot: no visible global function definition for ‘getDefaultAttrs’
GOplot: no visible global function definition for ‘agopen’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getNodeCenter’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘pieGlyph’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getX’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getY’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getNodeLW’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘drawTxtLabel’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘txtLabel’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘AgNode’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for ‘name’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for ‘getNodeCenter’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘getNodeXY’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘getY’
GOplot.counts: no visible global function definition for
  ‘getDefaultAttrs’
GOplot.counts: no visible global function definition for ‘agopen’
getPvalues: no visible global function definition for ‘mt.teststat’
getPvalues: no visible global function definition for ‘mt.rawp2adjp’
printDOT: no visible global function definition for ‘getDefaultAttrs’
printDOT: no visible global function definition for ‘toDot’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.LOOKUP’
initialize,classicExpr: no visible global function definition for
  ‘error’
scoresInTerm,topGOdata-missing: no visible global function definition
  for ‘scoreInNode’
Undefined global functions or variables:
  .PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error
  getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY
  mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel
* 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 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 ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘topGO.Rnw’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘topGO.Rnw’
  ...
	( 7711 GO terms found. )

Build GO DAG topology ..........
	( 11555 GO terms and 26037 relations. )

Annotating nodes ...............
	( 3889 genes annotated to the GO terms. )
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘topGO.Rnw’ using Sweave

Loading required package: xtable
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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: ‘topGO’

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

    members

Loading required package: org.Hs.eg.db



Building most specific GOs .....
Warning in result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
	( 1676 GO terms found. )

Build GO DAG topology ..........
	( 4372 GO terms and 9730 relations. )

Annotating nodes ...............
	( 314 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 884 nontrivial nodes
		 parameters: 
			 test statistic: fisher

			 -- Classic Algorithm -- 

		 the algorithm is scoring 968 nontrivial nodes
		 parameters: 
			 test statistic: ks
			 score order: increasing

			 -- Elim Algorithm -- 

		 the algorithm is scoring 968 nontrivial nodes
		 parameters: 
			 test statistic: ks
			 cutOff: 0.01
			 score order: increasing

	 Level 16:	1 nodes to be scored	(0 eliminated genes)

	 Level 15:	1 nodes to be scored	(0 eliminated genes)

	 Level 14:	2 nodes to be scored	(0 eliminated genes)

	 Level 13:	9 nodes to be scored	(25 eliminated genes)

	 Level 12:	19 nodes to be scored	(45 eliminated genes)

	 Level 11:	30 nodes to be scored	(45 eliminated genes)

	 Level 10:	58 nodes to be scored	(45 eliminated genes)

	 Level 9:	84 nodes to be scored	(55 eliminated genes)

	 Level 8:	117 nodes to be scored	(75 eliminated genes)

	 Level 7:	149 nodes to be scored	(149 eliminated genes)

	 Level 6:	169 nodes to be scored	(162 eliminated genes)

	 Level 5:	162 nodes to be scored	(174 eliminated genes)

	 Level 4:	101 nodes to be scored	(201 eliminated genes)

	 Level 3:	50 nodes to be scored	(214 eliminated genes)

	 Level 2:	15 nodes to be scored	(225 eliminated genes)

	 Level 1:	1 nodes to be scored	(225 eliminated genes)
Loading required package: Rgraphviz
Loading required package: grid

Attaching package: ‘grid’

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

    depth


Attaching package: ‘Rgraphviz’

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

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to


Building most specific GOs .....
	( 109 GO terms found. )

Build GO DAG topology ..........
	( 220 GO terms and 284 relations. )

Annotating nodes ...............
	( 86 genes annotated to the GO terms. )
Loading required package: multtest

Building most specific GOs .....
	( 7711 GO terms found. )

Build GO DAG topology ..........
	( 11555 GO terms and 26037 relations. )

Annotating nodes ...............
	( 3889 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 4045 nontrivial nodes
		 parameters: 
			 test statistic: Fisher test

			 -- Classic Algorithm -- 

		 the algorithm is scoring 5851 nontrivial nodes
		 parameters: 
			 test statistic: KS tests
			 score order: increasing
Killed

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

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL topGO
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘topGO’ ...
** 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (topGO)