Error using funguild_assign. Help?

[isaaceckert]

Hi Brendan! Huge fan of the FUNGuildR package! I've used it a lot over the past few years and have never had any issues. Recently I am getting this error when i try to use the funguild_assign command? I even tried it with the sample data (sample_fungi) and got the same error. The output is below!

sample_guilds <- funguild_assign(sample_fungi)
Error: parse error: trailing garbage
          p://www.lichenicolous.net))"},{"taxon":"Aaosphaeria","guid":
                     (right here) ------^

Any help is appreciated! Thanks so much!

[brendanf]

Hi Isaac!

Try updating FUNGuildR (remotes::install_github("brendanf/FUNGuildR")) and try again. FUNGuild changed their database format a bit a few months ago and I had to make an update. If that doesn't solve it, I'll look into it more.

[isaaceckert]

I uninstalled and reinstalled via remotes::install_github("brendanf/FUNGuildR") but i still get the same error?

[brendanf]

It looks like the error is coming during JSON parsing. Unfortunately I'm not able to replicate it myself.

Just to make sure, can you try funguild_assign(sample_fungi, funguild_testdb)? That uses a tiny local version of the database which includes only the sample fungi, so it should work unless there is another problem.

Then can you give me the output of sessionInfo()?

[isaaceckert]

Ok so funguild_assign(sample_fungi, funguild_testdb) worked! But just the command funguild_assign(sample_fungi)still doesnt. Here is the session output:

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
 [1] FUNGuildR_0.1.0.9999        tyRa_0.1.0                  reltools_0.1.0              betapart_1.5.2             
 [5] cowplot_1.1.1               speedyseq_0.1.2.9008        tibble_3.0.5                ShortRead_1.42.0           
 [9] GenomicAlignments_1.20.1    SummarizedExperiment_1.14.1 DelayedArray_0.10.0         matrixStats_0.57.0         
[13] Biobase_2.44.0              Rsamtools_2.0.3             GenomicRanges_1.36.1        GenomeInfoDb_1.20.0        
[17] BiocParallel_1.20.1         Hmisc_4.4-2                 ggplot2_3.3.3               Formula_1.2-4              
[21] minpack.lm_1.2-1            ade4_1.7-16                 fastDummies_1.6.3           relaimpo_2.2-3             
[25] mitools_2.4                 survey_4.0                  survival_3.2-7              Matrix_1.3-2               
[29] boot_1.3-27                 MASS_7.3-53                 ecodist_2.0.7               tidyr_1.1.2                
[33] picante_1.8.2               nlme_3.1-148                vegan_2.5-7                 lattice_0.20-41            
[37] permute_0.9-5               missForest_1.4              itertools_0.1-3             iterators_1.0.13           
[41] foreach_1.5.1               randomForest_4.6-14         seqinr_4.2-5                ggtree_1.16.6              
[45] seqRFLP_1.0.1               dada2_1.12.1                Rcpp_1.0.6                  DECIPHER_2.12.0            
[49] RSQLite_2.2.3               bios2mds_1.2.3              rgl_0.104.16                cluster_2.1.0              
[53] scales_1.1.1                e1071_1.7-4                 amap_0.8-18                 dplyr_1.0.0                
[57] BiocStyle_2.12.0            phangorn_2.5.5              ape_5.4                     msa_1.16.0                 
[61] Biostrings_2.52.0           XVector_0.24.0              IRanges_2.18.3              S4Vectors_0.22.1           
[65] BiocGenerics_0.32.0         phyloseq_1.28.0            

loaded via a namespace (and not attached):
  [1] utf8_1.1.4              tidyselect_1.1.0        htmlwidgets_1.5.3       devtools_2.3.2          munsell_0.5.0          
  [6] codetools_0.2-18        miniUI_0.1.1.1          withr_2.4.0             colorspace_2.0-0        knitr_1.30             
 [11] rstudioapi_0.13         geometry_0.4.5          labeling_0.4.2          GenomeInfoDbData_1.2.2  hwriter_1.3.2          
 [16] bit64_4.0.5             farver_2.0.3            rhdf5_2.28.1            rprojroot_2.0.2         vctrs_0.3.5            
 [21] treeio_1.8.2            generics_0.1.0          xfun_0.20               R6_2.5.0                doParallel_1.0.16      
 [26] manipulateWidget_0.10.1 bitops_1.0-6            assertthat_0.2.1        promises_1.1.1          nnet_7.3-15            
 [31] gtable_0.3.0            processx_3.4.5          rlang_0.4.10            splines_3.6.3           lazyeval_0.2.2         
 [36] checkmate_2.0.0         BiocManager_1.30.10     yaml_2.2.1              reshape2_1.4.4          abind_1.4-5            
 [41] crosstalk_1.1.1         backports_1.2.1         httpuv_1.5.4            usethis_2.0.0           tools_3.6.3            
 [46] ellipsis_0.3.1          biomformat_1.12.0       RColorBrewer_1.1-2      sessioninfo_1.1.1       plyr_1.8.5             
 [51] base64enc_0.1-3         progress_1.2.2          zlibbioc_1.32.0         purrr_0.3.4             RCurl_1.98-1.2         
 [56] ps_1.5.0                prettyunits_1.1.1       rpart_4.1-15            fs_1.5.0                magrittr_2.0.1         
 [61] data.table_1.13.6       pkgload_1.1.0           hms_1.0.0               mime_0.10               evaluate_0.14          
 [66] xtable_1.8-4            jpeg_0.1-8.1            gridExtra_2.3           testthat_3.0.1          compiler_3.6.3         
 [71] crayon_1.4.1            htmltools_0.5.1.1       mgcv_1.8-33             corpcor_1.6.9           later_1.1.0.1          
 [76] RcppParallel_5.0.2      DBI_1.1.1               magic_1.5-9             cli_2.3.0               quadprog_1.5-8         
 [81] igraph_1.2.6            pkgconfig_2.0.3         rvcheck_0.1.8           phylotools_0.2.2        foreign_0.8-75         
 [86] multtest_2.40.0         webshot_0.5.2           callr_3.5.1             stringr_1.4.0           digest_0.6.27          
 [91] rcdd_1.2-2              rmarkdown_2.6           fastmatch_1.1-0         tidytree_0.3.3          htmlTable_2.1.0        
 [96] curl_4.3                shiny_1.5.0             lifecycle_0.2.0         jsonlite_1.7.2          Rhdf5lib_1.6.3         
[101] desc_1.2.0              fansi_0.4.2             pillar_1.4.7            fastmap_1.0.1           httr_1.4.2             
[106] pkgbuild_1.2.0          remotes_2.2.0           glue_1.4.2              png_0.1-7               bit_4.0.4              
[111] class_7.3-18            stringi_1.5.3           blob_1.2.1              latticeExtra_0.6-29     memoise_1.1.0   

[isaaceckert]

Hey! So I actually went back and updated all the packages (i guess some of them had locks I didnt see) and when I reinstalled FUNguild it worked! Thanks for your help!

[brendanf]

Great to hear! Enjoy your FUNGuilding!

[brendanf]

In case anyone else with the same problem sees this, the solution that finally worked was to update other R packages and install the latest version of FUNGuildR.

[brendanf]

Hi @yuwingjane,
That is definitely an odd result. As I understand it, "Highly Probable" only makes sense if the guild (and therefore the trophic mode) is well defined. You can check the "notes" and "citationSource" columns to get more info about your particular case. I'm not directly involved in maintaining the FUNGuild database, but I will make an issue there to address it.

[brendanf]

@yuwingjane Looking at the two possibilities, my personal interpretation would be that Pichia should be "Possible" instead of "Highly Probable", and Caliciaceae should be "Probable" and "Symbiotroph".

[yuwingjane]

Hi Brendanf, thanks for your reply. This is not an occasional result. For example, I have 179 taxa belonging to Pathotroph-Saprotroph, 110 taxa belonging to Pathotroph-Saprotroph-Symbiotroph, 29 taxa belonging to Pathotroph-Symbiotroph, and 110 taxa belonging to Saprotroph-Symbiotroph. My question is which trophic mode should I assign each of these taxa to? Why would a taxon be assigned more than two trophic modes? Is it because it can have two or more living styles or because of some other reasons?

[yuwingjane]

All the above results are 'probable' or 'highly probable'.

[brendanf]

Ah, ok, I was specifically searching for "Pathotroph-Saprotroph-Symbiotroph" and "Highly Probably", and I only found two of those. This is an interesting question that other people will also run into, so I'm going to start a new conversation about it.