Hi,

I run into the following error using topGO_2.29.0:

running

library(org.Mm.eg.db)
library(topGO)

x <- org.Mm.egGO
mapped_genes <- mappedkeys(x)

set.seed(14)
de <- sample(mapped_genes, 100)

alg <- factor(as.integer(mapped_genes %in% de))
names(alg) <- mapped_genes

tgd <- new( "topGOdata", ontology="BP", allGenes = alg,
            annot=annFUN.org, mapping="org.Mm.eg.db")

gives this output/error:

Building most specific GOs .....
    ( 11603 GO terms found. )

Build GO DAG topology ..........
    ( 15489 GO terms and 37201 relations. )
Error in t(graph2SparseM(dirGraph, useWeights)) :
  object 'f_csrcsc2' not found

output of traceback():

9: t(graph2SparseM(dirGraph, useWeights))
8: t(graph2SparseM(dirGraph, useWeights))
7: sparseM2Graph(t(graph2SparseM(dirGraph, useWeights)), nodNames,
       edgemode = "directed")
6: reverseArch(dag)
5: buildLevels(g, leafs2root = TRUE)
4: .local(.Object, ...)
3: initialize(value, ...)
2: initialize(value, ...)
1: new("topGOdata", ontology = "BP", allGenes = alg, annot = annFUN.org,
       mapping = "org.Mm.eg.db")

sessionInfo:

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_GB.UTF-8  
[6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] topGO_2.29.0         SparseM_1.77         GO.db_3.4.1          graph_1.55.0         org.Mm.eg.db_3.4.1   AnnotationDbi_1.39.1 IRanges_2.11.5     
[8] S4Vectors_0.15.4     Biobase_2.37.2       BiocGenerics_0.23.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.11         bit_1.1-12           lattice_0.20-35      rlang_0.1.1          blob_1.1.0           tools_3.4.0          grid_3.4.0         
[8] DBI_0.7              matrixStats_0.52.2   bit64_0.9-7          digest_0.6.12        tibble_1.3.3         GOSemSim_2.3.1       memoise_1.1.0      
[15] RSQLite_2.0          BiocInstaller_1.27.2 compiler_3.4.0       pkgconfig_2.0.1    

thanks a lot for your help and suggestions,

Florian