I’m using the R package of MicrobiomeAnalystR 2.0.
I’ve also used 1.0 version without any errors.
But now the 2.0 version reports errors even at the initiation stage. I used the official sample data file " Mammalian Gut".
The mbSet object is always “1”.
As following:
mbSet<-Init.mbSetObj()
[1] “Init MicrobiomeAnalyst!”
Warning message:
In Cairo::CairoFonts(“Arial:style=Regular”, “Arial:style=Bold”, :
CairoFonts() has no effect on Windows. Please use par(family=“…”) to specify the desired font - see ?par.
mbSet<-SetModuleType(mbSet, “mdp”)
Warning message:
In mbSetObj$module.type ← nm : Coercing LHS to a list
mbSet<-Read16SAbundData(mbSet, “gordian_otu.txt”,“text”,“SILVA”,“F”,“false”)
Error in mbSetObj$module.type : $ operator is invalid for atomic vectors
mbSet<-ReadSampleTable(mbSet, “gordian_sampl.txt”)
Error in mbSetObj$module.type : $ operator is invalid for atomic vectors
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_Hong Kong SAR.utf8 LC_CTYPE=English_Hong Kong SAR.utf8
[3] LC_MONETARY=English_Hong Kong SAR.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Hong Kong SAR.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.4.1 Cairo_1.6-0 MicrobiomeAnalystR_2.0 phyloseq_1.42.0
I have this error message when loading the Microbiomeanalyst package
library(MicrobiomeAnalystR)
Loading required package: phyloseq
There were 32 warnings (use warnings() to see them)
warnings()
Warning messages:
1: replacing previous import ‘MASS::area’ by ‘genefilter::area’ when loading ‘MicrobiomeAnalystR’
2: replacing previous import ‘ape::ring’ by ‘igraph::ring’ when loading ‘MicrobiomeAnalystR’
3: replacing previous import ‘ape::edges’ by ‘igraph::edges’ when loading ‘MicrobiomeAnalystR’
4: replacing previous import ‘ape::mst’ by ‘igraph::mst’ when loading ‘MicrobiomeAnalystR’
5: replacing previous import ‘ape::degree’ by ‘igraph::degree’ when loading ‘MicrobiomeAnalystR’
6: replacing previous import ‘ape::complement’ by ‘metacoder::complement’ when loading ‘MicrobiomeAnalystR’
7: replacing previous import ‘igraph::hierarchy’ by ‘metacoder::hierarchy’ when loading ‘MicrobiomeAnalystR’
8: replacing previous import ‘ggplot2::map_data’ by ‘metacoder::map_data’ when loading ‘MicrobiomeAnalystR’
9: replacing previous import ‘edgeR::calcNormFactors’ by ‘metagenomeSeq::calcNormFactors’ when loading ‘MicrobiomeAnalystR’
10: replacing previous import ‘metacoder::filter_taxa’ by ‘phyloseq::filter_taxa’ when loading ‘MicrobiomeAnalystR’
11: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘MicrobiomeAnalystR’
12: replacing previous import ‘gridExtra::combine’ by ‘randomForest::combine’ when loading ‘MicrobiomeAnalystR’
13: replacing previous import ‘data.table::melt’ by ‘reshape::melt’ when loading ‘MicrobiomeAnalystR’
14: replacing previous import ‘metacoder::is_root’ by ‘taxa::is_root’ when loading ‘MicrobiomeAnalystR’
15: replacing previous import ‘metacoder::is_stem’ by ‘taxa::is_stem’ when loading ‘MicrobiomeAnalystR’
16: replacing previous import ‘igraph::as_data_frame’ by ‘taxa::as_data_frame’ when loading ‘MicrobiomeAnalystR’
17: replacing previous import ‘metacoder::n_subtaxa’ by ‘taxa::n_subtaxa’ when loading ‘MicrobiomeAnalystR’
18: replacing previous import ‘metacoder::is_internode’ by ‘taxa::is_internode’ when loading ‘MicrobiomeAnalystR’
19: replacing previous import ‘metacoder::taxon’ by ‘taxa::taxon’ when loading ‘MicrobiomeAnalystR’
20: replacing previous import ‘metacoder::internodes’ by ‘taxa::internodes’ when loading ‘MicrobiomeAnalystR’
21: replacing previous import ‘metacoder::taxon_id’ by ‘taxa::taxon_id’ when loading ‘MicrobiomeAnalystR’
22: replacing previous import ‘metacoder::subtaxa’ by ‘taxa::subtaxa’ when loading ‘MicrobiomeAnalystR’
23: replacing previous import ‘metacoder::n_supertaxa’ by ‘taxa::n_supertaxa’ when loading ‘MicrobiomeAnalystR’
24: replacing previous import ‘metacoder::taxon_rank’ by ‘taxa::taxon_rank’ when loading ‘MicrobiomeAnalystR’
25: replacing previous import ‘metacoder::stems’ by ‘taxa::stems’ when loading ‘MicrobiomeAnalystR’
26: replacing previous import ‘metacoder::leaves’ by ‘taxa::leaves’ when loading ‘MicrobiomeAnalystR’
27: replacing previous import ‘metacoder::n_leaves’ by ‘taxa::n_leaves’ when loading ‘MicrobiomeAnalystR’
28: replacing previous import ‘metacoder::roots’ by ‘taxa::roots’ when loading ‘MicrobiomeAnalystR’
29: replacing previous import ‘metacoder::taxonomy’ by ‘taxa::taxonomy’ when loading ‘MicrobiomeAnalystR’
30: replacing previous import ‘metacoder::supertaxa’ by ‘taxa::supertaxa’ when loading ‘MicrobiomeAnalystR’
31: replacing previous import ‘metacoder::is_leaf’ by ‘taxa::is_leaf’ when loading ‘MicrobiomeAnalystR’
32: replacing previous import ‘igraph::diversity’ by ‘vegan::diversity’ when loading ‘MicrobiomeAnalystR’
I also had problems installing the MicrobiomeAnalyst package. I had to download Cairo, qiime, biom, and Tax4Fun packages directly from CRAN and installed them manually.
Hi all,
We have fixed this issue. You can re-install MicrobiomeAnalystR and it should work. Please let know in case you have more questions.
Hope this helps!