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moosa-r / rbioapi

rbioapi: User-Friendly R Interface to Biologic Web Services' API
https://rbioapi.moosa-r.com/
GNU General Public License v3.0
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Error running example line of code from ?rba_panther_enrich #13

Closed erzakiev closed 1 year ago

erzakiev commented 1 year ago

In rbioapi_0.7.9 I get the following error while trying to run the example line of code from ?rba_panther_enrich man page:

> rba_panther_enrich(genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
+                              "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
+                    organism = 9606, annot_dataset = "GO:0008150",
+                    cutoff = 0.01)
Performing over-representation enrichment analysis of 10 input genes of organism 9606 against GO:0008150 datasets.

$search
$search$error
[1] "Error annotation type data set not specified"

$search$search_type
[1] "overrepresentation"

Session information:

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rbioapi_0.7.9         shiny_1.7.4.1         clustermole_1.1.0     GSEABase_1.60.0      
 [5] graph_1.76.0          annotate_1.76.0       XML_3.99-0.14         AnnotationDbi_1.60.2 
 [9] IRanges_2.32.0        S4Vectors_0.36.2      Biobase_2.58.0        BiocGenerics_0.44.0  
[13] dplyr_1.1.2           clusterProfiler_4.6.2 msigdbr_7.5.1         cerebroApp_1.3.1     
[17] presto_1.0.0          data.table_1.14.8     Rcpp_1.0.11           SeuratObject_4.1.3   
[21] Seurat_4.3.0.1       

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3              scattermore_1.2             tidyr_1.3.0                
  [4] ggplot2_3.4.2               bit64_4.0.5                 irlba_2.3.5.1              
  [7] DelayedArray_0.24.0         KEGGREST_1.38.0             RCurl_1.98-1.12            
 [10] generics_0.1.3              ScaledMatrix_1.6.0          cowplot_1.1.1              
 [13] RSQLite_2.3.1               shadowtext_0.1.2            RANN_2.6.1                 
 [16] future_1.33.0               bit_4.0.5                   tzdb_0.4.0                 
 [19] enrichplot_1.18.4           spatstat.data_3.0-1         xml2_1.3.5                 
 [22] httpuv_1.6.11               SummarizedExperiment_1.28.0 fontawesome_0.5.1          
 [25] viridis_0.6.3               hms_1.1.3                   jquerylib_0.1.4            
 [28] babelgene_22.9              promises_1.2.0.1            fansi_1.0.4                
 [31] progress_1.2.2              dbplyr_2.3.3                igraph_1.5.0               
 [34] DBI_1.1.3                   htmlwidgets_1.6.2           spatstat.geom_3.2-2        
 [37] purrr_1.0.1                 ellipsis_0.3.2              crosstalk_1.2.0            
 [40] biomaRt_2.54.1              deldir_1.0-9                sparseMatrixStats_1.10.0   
 [43] MatrixGenerics_1.10.0       vctrs_0.6.3                 SingleCellExperiment_1.20.1
 [46] ROCR_1.0-11                 abind_1.4-5                 cachem_1.0.8               
 [49] withr_2.5.0                 ggforce_0.4.1               HDO.db_0.99.1              
 [52] progressr_0.13.0            vroom_1.6.3                 sctransform_0.3.5          
 [55] treeio_1.22.0               prettyunits_1.1.1           goftest_1.2-3              
 [58] cluster_2.1.4               DOSE_3.24.2                 ape_5.7-1                  
 [61] lazyeval_0.2.2              crayon_1.5.2                spatstat.explore_3.2-1     
 [64] edgeR_3.40.2                pkgconfig_2.0.3             tweenr_2.0.2               
 [67] GenomeInfoDb_1.34.9         nlme_3.1-162                rlang_1.1.1                
 [70] globals_0.16.2              lifecycle_1.0.3             miniUI_0.1.1.1             
 [73] colourpicker_1.2.0          downloader_0.4              filelock_1.0.2             
 [76] BiocFileCache_2.6.1         rsvd_1.0.5                  polyclip_1.10-4            
 [79] GSVA_1.46.0                 matrixStats_1.0.0           lmtest_0.9-40              
 [82] shinyFiles_0.9.3            Matrix_1.6-0                aplot_0.1.10               
 [85] singscore_1.18.0            Rhdf5lib_1.20.0             zoo_1.8-12                 
 [88] ggridges_0.5.4              png_0.1-8                   viridisLite_0.4.2          
 [91] bitops_1.0-7                shinydashboard_0.7.2        gson_0.1.0                 
 [94] KernSmooth_2.23-22          rhdf5filters_1.10.1         Biostrings_2.66.0          
 [97] blob_1.2.4                  DelayedMatrixStats_1.20.0   stringr_1.5.0              
[100] qvalue_2.30.0               parallelly_1.36.0           spatstat.random_3.1-5      
[103] readr_2.1.4                 gridGraphics_0.5-1          beachmat_2.14.2            
[106] scales_1.2.1                memoise_2.0.1               magrittr_2.0.3             
[109] plyr_1.8.8                  ica_1.0-3                   zlibbioc_1.44.0            
[112] compiler_4.2.2              scatterpie_0.2.1            RColorBrewer_1.1-3         
[115] fitdistrplus_1.1-11         cli_3.6.1                   XVector_0.38.0             
[118] listenv_0.9.0               patchwork_1.1.2             pbapply_1.7-2              
[121] MASS_7.3-60                 tidyselect_1.2.0            stringi_1.7.12             
[124] yaml_2.3.7                  GOSemSim_2.24.0             locfit_1.5-9.8             
[127] BiocSingular_1.14.0         ggrepel_0.9.3               grid_4.2.2                 
[130] sass_0.4.7                  fastmatch_1.1-3             tools_4.2.2                
[133] future.apply_1.11.0         parallel_4.2.2              rstudioapi_0.15.0          
[136] gridExtra_2.3               farver_2.1.1                Rtsne_0.16                 
[139] ggraph_2.1.0                BiocManager_1.30.21.1       digest_0.6.33              
[142] GenomicRanges_1.50.2        later_1.3.1                 RcppAnnoy_0.0.21           
[145] shinyWidgets_0.7.6          httr_1.4.6                  colorspace_2.1-0           
[148] fs_1.6.2                    tensor_1.5                  reticulate_1.30            
[151] splines_4.2.2               uwot_0.1.16                 yulab.utils_0.0.6          
[154] tidytree_0.4.4              spatstat.utils_3.0-3        graphlayouts_1.0.0         
[157] sp_2.0-0                    ggplotify_0.1.1             plotly_4.10.2              
[160] xtable_1.8-4                jsonlite_1.8.7              ggtree_3.6.2               
[163] tidygraph_1.2.3             ggfun_0.1.1                 R6_2.5.1                   
[166] pillar_1.9.0                htmltools_0.5.5             mime_0.12                  
[169] glue_1.6.2                  fastmap_1.1.1               DT_0.28                    
[172] BiocParallel_1.32.6         codetools_0.2-19            fgsea_1.24.0               
[175] utf8_1.2.3                  lattice_0.21-8              bslib_0.5.0                
[178] spatstat.sparse_3.0-2       tibble_3.2.1                curl_5.0.1                 
[181] leiden_0.4.3                GO.db_3.16.0                shinyjs_2.1.0              
[184] limma_3.54.2                survival_3.5-5              munsell_0.5.0              
[187] rhdf5_2.42.1                GenomeInfoDbData_1.2.9      HDF5Array_1.26.0           
[190] reshape2_1.4.4              gtable_0.3.3                shinycssloaders_1.0.0
erzakiev commented 1 year ago

rba_connection_test results are ok:

> rba_connection_test(print_output = TRUE)
Checking Your connection to the Databases currently supported by rbioapi:
--->>> Internet :
+++ Connected to the Internet.
--->>> Enrichr :
+++ The server is responding.
--->>> Ensembl :
+++ The server is responding.
--->>> JASPAR :
+++ The server is responding.
--->>> miEAA :
+++ The server is responding.
--->>> PANTHER :
+++ The server is responding.
--->>> Reactome Content Service :
+++ The server is responding.
--->>> Reactome Analysis Service :
+++ The server is responding.
--->>> STRING :
+++ The server is responding.
--->>> UniProt :
+++ The server is responding.
erzakiev commented 1 year ago

On R 4.3 and Windows the error is reproducible:

rba_panther_enrich(genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
+                              "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
+                    organism = 9606, annot_dataset = "GO:0008150",
+                    cutoff = 0.01)
Performing over-representation enrichment analysis of 10 input genes of organism 9606 against GO:0008150 datasets.
$search
$search$error
[1] "Error annotation type data set not specified"

$search$search_type
[1] "overrepresentation"
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Paris
tzcode source: internal

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

other attached packages:
[1] rbioapi_0.7.9

loaded via a namespace (and not attached):
  [1] DBI_1.1.3                   bitops_1.0-7                remotes_2.4.2.1            
  [4] rlang_1.1.1                 magrittr_2.0.3              matrixStats_1.0.0          
  [7] compiler_4.3.1              RSQLite_2.3.1               png_0.1-8                  
 [10] callr_3.7.3                 vctrs_0.6.3                 stringr_1.5.0              
 [13] profvis_0.3.8               pkgconfig_2.0.3             crayon_1.5.2               
 [16] fastmap_1.1.1               XVector_0.40.0              ellipsis_0.3.2             
 [19] utf8_1.2.3                  promises_1.2.0.1            rmarkdown_2.23             
 [22] sessioninfo_1.2.2           decoupleR_2.6.0             ps_1.7.5                   
 [25] purrr_1.0.1                 bit_4.0.5                   xfun_0.39                  
 [28] zlibbioc_1.46.0             cachem_1.0.8                jsonlite_1.8.7             
 [31] GenomeInfoDb_1.36.1         blob_1.2.4                  later_1.3.1                
 [34] DelayedArray_0.26.7         BiocParallel_1.34.2         parallel_4.3.1             
 [37] prettyunits_1.1.1           R6_2.5.1                    stringi_1.7.12             
 [40] pkgload_1.3.2.1             GenomicRanges_1.52.0        Rcpp_1.0.11                
 [43] SummarizedExperiment_1.30.2 knitr_1.43                  usethis_2.2.2              
 [46] IRanges_2.34.1              httpuv_1.6.11               Matrix_1.5-4.1             
 [49] tidyselect_1.2.0            rstudioapi_0.15.0           abind_1.4-5                
 [52] codetools_0.2-19            miniUI_0.1.1.1              curl_5.0.1                 
 [55] processx_3.8.2              pkgbuild_1.4.2              lattice_0.21-8             
 [58] tibble_3.2.1                Biobase_2.60.0              shiny_1.7.5                
 [61] KEGGREST_1.40.0             evaluate_0.21               desc_1.4.2                 
 [64] urlchecker_1.0.1            Biostrings_2.68.1           BiocManager_1.30.22        
 [67] pillar_1.9.0                MatrixGenerics_1.12.3       DT_0.28                    
 [70] stats4_4.3.1                shinyjs_2.1.0               generics_0.1.3             
 [73] rprojroot_2.0.3             RCurl_1.98-1.12             S4Vectors_0.38.1           
 [76] ggplot2_3.4.2               munsell_0.5.0               scales_1.2.1               
 [79] xtable_1.8-4                glue_1.6.2                  tools_4.3.1                
 [82] locfit_1.5-9.8              fs_1.6.3                    grid_4.3.1                 
 [85] tidyr_1.3.0                 devtools_2.4.5              AnnotationDbi_1.62.2       
 [88] colorspace_2.1-0            GenomeInfoDbData_1.2.10     cli_3.6.1                  
 [91] fansi_1.0.4                 S4Arrays_1.0.5              dplyr_1.1.2                
 [94] gtable_0.3.3                DESeq2_1.40.2               EnhancedVolcano_1.18.0     
 [97] digest_0.6.33               BiocGenerics_0.46.0         tximport_1.28.0            
[100] ggrepel_0.9.3               htmlwidgets_1.6.2           memoise_2.0.1              
[103] htmltools_0.5.5             lifecycle_1.0.3             httr_1.4.6                 
[106] mime_0.12                   bit64_4.0.5

The connection is ok as well

> rba_connection_test()
Checking Your connection to the Databases currently supported by rbioapi:
--->>> Internet :
+++ Connected to the Internet.
--->>> Enrichr :
+++ The server is responding.
--->>> Ensembl :
+++ The server is responding.
--->>> JASPAR :
+++ The server is responding.
--->>> miEAA :
+++ The server is responding.
--->>> PANTHER :
+++ The server is responding.
--->>> Reactome Content Service :
+++ The server is responding.
--->>> Reactome Analysis Service :
+++ The server is responding.
--->>> STRING :
+++ The server is responding.
--->>> UniProt :
+++ The server is responding.
moosa-r commented 1 year ago

Dear Emile,

Thank you for reporting this issue.

I'm sorry for the inconvenience. I've made minor fixes to reflect the recent changes in PANTHER's API in the past few weeks. You can reinstall rbioapi with the latest fix using the following commands: (I will submit it to CRAN when some changes accumulate)

install.packages("remotes")
remotes::install_github("moosa-r/rbioapi")

Hopefully, this will solve your problem.

Best, Moosa

erzakiev commented 1 year ago

works ok, amazing, thanks! I knew I should have tried the dev version first before posting, sorry!