Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:41 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for cellTree on merida1


To the developers/maintainers of the cellTree package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellTree.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 283/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellTree 1.26.0  (landing page)
David duVerle
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/cellTree
git_branch: RELEASE_3_15
git_last_commit: b234c33
git_last_commit_date: 2022-04-26 11:28:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: cellTree
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellTree
StartedAt: 2022-10-18 17:30:11 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 17:32:20 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 129.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellTree
###
##############################################################################
##############################################################################


* checking for file ‘cellTree/DESCRIPTION’ ... OK
* preparing ‘cellTree’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cellTree-vignette.Rnw’ using knitr
Loading required package: topGO
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, 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 namespace: maptpx


Building most specific GOs .....
	( 1580 GO terms found. )

Build GO DAG topology ..........
	( 1799 GO terms and 3022 relations. )

Annotating nodes ...............
	( 9903 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 794 nontrivial nodes
		 parameters: 
			 test statistic: KS
			 score order: decreasing

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	41 nodes to be scored	(13 eliminated genes)

	 Level 10:	100 nodes to be scored	(61 eliminated genes)

	 Level 9:	127 nodes to be scored	(793 eliminated genes)

	 Level 8:	112 nodes to be scored	(2317 eliminated genes)

	 Level 7:	105 nodes to be scored	(4010 eliminated genes)

	 Level 6:	104 nodes to be scored	(6540 eliminated genes)

	 Level 5:	86 nodes to be scored	(7569 eliminated genes)

	 Level 4:	58 nodes to be scored	(8915 eliminated genes)

	 Level 3:	52 nodes to be scored	(9580 eliminated genes)

	 Level 2:	2 nodes to be scored	(9806 eliminated genes)

	 Level 1:	1 nodes to be scored	(9860 eliminated genes)

Building most specific GOs .....
	( 1580 GO terms found. )

Build GO DAG topology ..........
	( 1799 GO terms and 3022 relations. )

Annotating nodes ...............
	( 9903 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 794 nontrivial nodes
		 parameters: 
			 test statistic: KS
			 score order: decreasing

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	41 nodes to be scored	(13 eliminated genes)

	 Level 10:	100 nodes to be scored	(61 eliminated genes)

	 Level 9:	127 nodes to be scored	(793 eliminated genes)

	 Level 8:	112 nodes to be scored	(2317 eliminated genes)

	 Level 7:	105 nodes to be scored	(4010 eliminated genes)

	 Level 6:	104 nodes to be scored	(6540 eliminated genes)

	 Level 5:	86 nodes to be scored	(7569 eliminated genes)

	 Level 4:	58 nodes to be scored	(8915 eliminated genes)

	 Level 3:	52 nodes to be scored	(9580 eliminated genes)

	 Level 2:	2 nodes to be scored	(9806 eliminated genes)

	 Level 1:	1 nodes to be scored	(9860 eliminated genes)

Building most specific GOs .....
	( 1580 GO terms found. )

Build GO DAG topology ..........
	( 1799 GO terms and 3022 relations. )

Annotating nodes ...............
	( 9903 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 794 nontrivial nodes
		 parameters: 
			 test statistic: KS
			 score order: decreasing

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	41 nodes to be scored	(13 eliminated genes)

	 Level 10:	100 nodes to be scored	(61 eliminated genes)

	 Level 9:	127 nodes to be scored	(793 eliminated genes)

	 Level 8:	112 nodes to be scored	(2317 eliminated genes)

	 Level 7:	105 nodes to be scored	(4010 eliminated genes)

	 Level 6:	104 nodes to be scored	(6540 eliminated genes)

	 Level 5:	86 nodes to be scored	(7569 eliminated genes)

	 Level 4:	58 nodes to be scored	(8915 eliminated genes)

	 Level 3:	52 nodes to be scored	(9580 eliminated genes)

	 Level 2:	2 nodes to be scored	(9806 eliminated genes)

	 Level 1:	1 nodes to be scored	(9860 eliminated genes)

Building most specific GOs .....
	( 1580 GO terms found. )

Build GO DAG topology ..........
	( 1799 GO terms and 3022 relations. )

Annotating nodes ...............
	( 9903 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 794 nontrivial nodes
		 parameters: 
			 test statistic: KS
			 score order: decreasing

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	41 nodes to be scored	(13 eliminated genes)

	 Level 10:	100 nodes to be scored	(61 eliminated genes)

	 Level 9:	127 nodes to be scored	(793 eliminated genes)

	 Level 8:	112 nodes to be scored	(2317 eliminated genes)

	 Level 7:	105 nodes to be scored	(4010 eliminated genes)

	 Level 6:	104 nodes to be scored	(6540 eliminated genes)

	 Level 5:	86 nodes to be scored	(7569 eliminated genes)

	 Level 4:	58 nodes to be scored	(8915 eliminated genes)

	 Level 3:	52 nodes to be scored	(9580 eliminated genes)

	 Level 2:	2 nodes to be scored	(9806 eliminated genes)

	 Level 1:	1 nodes to be scored	(9860 eliminated genes)

Building most specific GOs .....
	( 1580 GO terms found. )

Build GO DAG topology ..........
	( 1799 GO terms and 3022 relations. )

Annotating nodes ...............
	( 9903 genes annotated to the GO terms. )

			 -- Weight01 Algorithm -- 

		 the algorithm is scoring 794 nontrivial nodes
		 parameters: 
			 test statistic: KS
			 score order: decreasing

	 Level 13:	1 nodes to be scored	(0 eliminated genes)

	 Level 12:	5 nodes to be scored	(0 eliminated genes)

	 Level 11:	41 nodes to be scored	(13 eliminated genes)

	 Level 10:	100 nodes to be scored	(61 eliminated genes)

	 Level 9:	127 nodes to be scored	(793 eliminated genes)

	 Level 8:	112 nodes to be scored	(2317 eliminated genes)

	 Level 7:	105 nodes to be scored	(4010 eliminated genes)

	 Level 6:	104 nodes to be scored	(6540 eliminated genes)

	 Level 5:	86 nodes to be scored	(7569 eliminated genes)

	 Level 4:	58 nodes to be scored	(8915 eliminated genes)

	 Level 3:	52 nodes to be scored	(9580 eliminated genes)

	 Level 2:	2 nodes to be scored	(9806 eliminated genes)

	 Level 1:	1 nodes to be scored	(9860 eliminated genes)
Quitting from lines 348-352 (cellTree-vignette.Rnw) 
Error: processing vignette 'cellTree-vignette.Rnw' failed with diagnostics:
At core/layout/fruchterman_reingold.c:401 : Weights must be positive for Fruchterman-Reingold layout. Invalid value
--- failed re-building ‘cellTree-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘cellTree-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted