Unexpected error with topGO, cannot build topGOdata object
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abf ▴ 30
@abf-14661
Last seen 2.3 years ago
United States

When I try and create the topGOdata object, I get an error warning about a zero-length vector. I've recently moved to a Mac (see session info). Previously I had no issues using topGO on a linux box, under R-3.6.3 (with an up to date bioconductor). I was hoping someone might have gotten a similar error and could help me troubleshoot? I'm not certain where to start looking.

Quick Start Example from the vignette:

>  library(topGO)
>  library(ALL)
>  data(ALL)
>  data(geneList)
> 
>  affyLib <- paste(annotation(ALL), "db", sep = ".")
>  library(package = affyLib, character.only = TRUE)
>  
>  sampleGOdata <- new("topGOdata",
+                      description = "Simple session", ontology = "BP",
+                      allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10,
+                      annot = annFUN.db, affyLib = affyLib)

Building most specific GOs .....
    ( 1647 GO terms found. )

Build GO DAG topology ..........
Error in if (node == GENE.ONTO.ROOT) return(2) : 
  argument is of length zero

There is also a warning message:

> warnings()
Warning message:
In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

Session Info:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices
[6] utils     datasets  methods   base     

other attached packages:
 [1] hgu95av2.db_3.2.3    org.Hs.eg.db_3.11.0 
 [3] ALL_1.29.0           org.Mm.eg.db_3.11.0 
 [5] topGO_2.40.0         SparseM_1.78        
 [7] GO.db_3.11.0         AnnotationDbi_1.50.0
 [9] IRanges_2.22.1       S4Vectors_0.26.0    
[11] Biobase_2.48.0       graph_1.66.0        
[13] BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       bit_1.1-15.2       lattice_0.20-41   
 [4] rlang_0.4.6        blob_1.2.1         tools_4.0.0       
 [7] grid_4.0.0         DBI_1.1.0          matrixStats_0.56.0
[10] bit64_0.9-7        digest_0.6.25      vctrs_0.2.4       
[13] memoise_1.1.0      RSQLite_2.2.0      compiler_4.0.0    
[16] pkgconfig_2.0.3
topGO • 1.3k views
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0
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I think that the issue may be with the new GO.db package, as elaborated here:

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1
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There may be an issue with that, but I just ran the code using R-4.0.0 and Bioc11 and it works for me on Windows. So I sort of doubt the issue is any problems with GO.db (although there may be other silent issues).

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e.g.

> sampleGOdata <- new("topGOdata",
+                       description = "Simple session", ontology = "BP",
+                       allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10,
+                       annot = annFUN.db, affyLib = affyLib)

Building most specific GOs .....
    ( 1647 GO terms found. )

Build GO DAG topology ..........
    ( 4545 GO terms and 10466 relations. )

Annotating nodes ...............
    ( 310 genes annotated to the GO terms. )
Warning message:
In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
> sampleGOdata

------------------------- topGOdata object -------------------------

 Description:
   -  Simple session 

 Ontology:
   -  BP 

 323 available genes (all genes from the array):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 50  significant genes. 

 310 feasible genes (genes that can be used in the analysis):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 46  significant genes. 

 GO graph (nodes with at least  10  genes):
   - a graph with directed edges
   - number of nodes = 1110 
   - number of edges = 2400 

------------------------- topGOdata object -------------------------

> sessionInfo()
R version 4.0.0 RC (2020-04-20 r78265)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] hgu95av2.db_3.2.3    org.Hs.eg.db_3.10.0  ALL_1.29.0          
 [4] topGO_2.39.1         SparseM_1.78         GO.db_3.10.0        
 [7] AnnotationDbi_1.49.1 IRanges_2.21.8       S4Vectors_0.25.15   
[10] Biobase_2.47.3       graph_1.65.3         BiocGenerics_0.33.3 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       bit_1.1-15.2       lattice_0.20-41    rlang_0.4.5       
 [5] blob_1.2.1         tools_4.0.0        grid_4.0.0         DBI_1.1.0         
 [9] matrixStats_0.56.0 bit64_0.9-7        digest_0.6.25      vctrs_0.2.4       
[13] memoise_1.1.0      RSQLite_2.2.0      compiler_4.0.0     pkgconfig_2.0.3
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Urp. Maybe it is a problem with the current GO.db package. The topGO package makes use of the old BiMap interface, and does this under the hood:

GOParents <- get(paste("GO", whichOnto, "PARENTS", sep = ""))
GENE.ONTO.ROOT <- as.character(revmap(GOParents)$all)

Which is the equivalent of

as.character(revmap(GOBPPARENTS)$all)

Which in previous versions gave

> as.character(revmap(GOBPPARENTS)$all)
[1] "GO:0008150"

## but now with the current version of GO.db it does

> as.character(revmap(GOBPPARENTS)$all)
character(0)

And this looks different as well

## old GO.db
> head(toTable(GOBPPARENTS))
       go_id      go_id RelationshipType
1 GO:0000001 GO:0048308             is_a
2 GO:0000001 GO:0048311             is_a
3 GO:0000002 GO:0007005             is_a
4 GO:0000003 GO:0008150             is_a
5 GO:0042254 GO:0022613             is_a
6 GO:0000011 GO:0007033             is_a

# New GO.db
> head(toTable(GOBPPARENTS))
       go_id      go_id RelationshipType
1 GO:0000002 GO:0032042          part of
2 GO:0000002 GO:0033955             is_a
3 GO:0000003 GO:0019953             is_a
4 GO:0000003 GO:0019954             is_a
5 GO:0000003 GO:0022414          part of
6 GO:0000003 GO:0032504             is_a

So let's wait for Kayla to update GO.db and that should make all this work again.

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Perhaps you can now re-try: https://support.bioconductor.org/p/130753/

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1
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Et voila

> library(topGO)
>  library(ALL)
>   data(ALL)
>   data(geneList)
>  
>   affyLib <- paste(annotation(ALL), "db", sep = ".")
>   library(package = affyLib, character.only = TRUE)
Loading required package: org.Hs.eg.db


>   
>   sampleGOdata <- new("topGOdata",
+                       description = "Simple session", ontology = "BP",
+                       allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10,
+                       annot = annFUN.db, affyLib = affyLib)

Building most specific GOs .....
    ( 1647 GO terms found. )

Build GO DAG topology ..........
    ( 4545 GO terms and 10466 relations. )

Annotating nodes ...............
    ( 310 genes annotated to the GO terms. )
Warning message:
In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
> sampleGOdata

------------------------- topGOdata object -------------------------

 Description:
   -  Simple session 

 Ontology:
   -  BP 

 323 available genes (all genes from the array):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 50  significant genes. 

 310 feasible genes (genes that can be used in the analysis):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 46  significant genes. 

 GO graph (nodes with at least  10  genes):
   - a graph with directed edges
   - number of nodes = 1110 
   - number of edges = 2400 

------------------------- topGOdata object -------------------------

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] hgu95av2.db_3.2.3    org.Hs.eg.db_3.11.1  ALL_1.30.0          
 [4] topGO_2.40.0         SparseM_1.78         graph_1.66.0        
 [7] GO.db_3.11.1         AnnotationDbi_1.50.0 IRanges_2.22.1      
[10] S4Vectors_0.26.0     Biobase_2.48.0       BiocGenerics_0.34.0 
[13] BiocManager_1.30.10 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       bit_1.1-15.2       lattice_0.20-41    rlang_0.4.6       
 [5] blob_1.2.1         tools_4.0.0        grid_4.0.0         DBI_1.1.0         
 [9] matrixStats_0.56.0 bit64_0.9-7        digest_0.6.25      vctrs_0.2.4       
[13] memoise_1.1.0      RSQLite_2.2.0      compiler_4.0.0     pkgconfig_2.0.3
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3
Entering edit mode
abf ▴ 30
@abf-14661
Last seen 2.3 years ago
United States

I updated GO.db using

BiocManager::install('GO.db')

topGO is now working properly for me. Thanks to Kayla for her update and Kevin and James for identifying the cause.

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