Error running netDx vignette 1 locally

[writingindy]

Description

Running the buildPredictor() function to generate the out variable causes an error when it tries to download genemania-netdx.jar from http://download.baderlab.org/netDx/java8/genemania-netdx.jar.

Steps to Recreate

1. Download R Script of vignette 1 (Building binary classifier from clinical and ’omic data using pathway-level features) from http://bioconductor.org/packages/release/bioc/html/netDx.html.
2. Run R Script.

Error Message on R

2021-09-13 14:43:35
Pearson similarity chosen - enforcing min. 5 patients per net.
adding rname 'http://download.baderlab.org/netDx/java8/genemania-netdx.jar'
  |=========================================================================================| 100%

Warning: download failed
  web resource path: 'http://download.baderlab.org/netDx/java8/genemania-netdx.jar'
  local file path: '~/Library/Caches/netDx/52e01aaec6d_genemania-netdx.jar'
  reason: Service Unavailable (HTTP 503).
Warning: bfcadd() failed; resource removed
  rid: BFC3
  fpath: 'http://download.baderlab.org/netDx/java8/genemania-netdx.jar'
  reason: download failed
Warning in value[[3L]](cond) :
  
trying to add rname 'http://download.baderlab.org/netDx/java8/genemania-netdx.jar' produced error:
  bfcadd() failed; see warnings()
Error in bfcrpath(bfc, fileURL) : not all 'rnames' found or unique. 

sessionInfo() Output

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.5.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] rhdf5_2.36.0                netDx_1.4.3                 clusterExperiment_2.11.3   
 [4] scater_1.20.1               scuttle_1.2.1               SingleCellExperiment_1.14.1
 [7] RColorBrewer_1.1-2          rappdirs_0.3.3              combinat_0.0-8             
[10] doParallel_1.0.16           iterators_1.0.13            foreach_1.5.1              
[13] bigmemory_4.5.36            GenomeInfoDbData_1.2.6      reshape2_1.4.4             
[16] httr_1.4.2                  igraph_1.2.6                glmnet_4.1-2               
[19] Matrix_1.3-4                RCy3_2.12.4                 ggplot2_3.3.5              
[22] pracma_2.3.3                ROCR_1.0-11                 Rtsne_0.15                 
[25] curatedTCGAData_1.14.0      MultiAssayExperiment_1.18.0 SummarizedExperiment_1.22.0
[28] Biobase_2.52.0              GenomicRanges_1.44.0        GenomeInfoDb_1.28.4        
[31] IRanges_2.26.0              S4Vectors_0.30.0            BiocGenerics_0.38.0        
[34] MatrixGenerics_1.4.3        matrixStats_0.60.1         

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                    R.utils_2.10.1                tidyselect_1.1.1             
  [4] RSQLite_2.2.8                 AnnotationDbi_1.54.1          grid_4.1.1                   
  [7] BiocParallel_1.26.2           RNeXML_2.4.5                  munsell_0.5.0                
 [10] ScaledMatrix_1.0.0            base64url_1.4                 codetools_0.2-18             
 [13] pbdZMQ_0.3-5                  withr_2.4.2                   colorspace_2.0-2             
 [16] filelock_1.0.2                dplR_1.7.2                    uuid_0.1-4                   
 [19] zinbwave_1.14.1               NMF_0.23.0                    repr_1.1.3                   
 [22] bit64_4.0.5                   vctrs_0.3.8                   generics_0.1.0               
 [25] BiocFileCache_2.0.0           R6_2.5.1                      ggbeeswarm_0.6.0             
 [28] netSmooth_1.12.0              rsvd_1.0.5                    RJSONIO_1.3-1.5              
 [31] locfit_1.5-9.4                bitops_1.0-7                  rhdf5filters_1.4.0           
 [34] cachem_1.0.6                  DelayedArray_0.18.0           assertthat_0.2.1             
 [37] promises_1.2.0.1              scales_1.1.1                  beeswarm_0.4.0               
 [40] gtable_0.3.0                  phylobase_0.8.10              beachmat_2.8.1               
 [43] rlang_0.4.11                  genefilter_1.74.0             splines_4.1.1                
 [46] lazyeval_0.2.2                BiocManager_1.30.16           yaml_2.2.1                   
 [49] backports_1.2.1               httpuv_1.6.3                  tools_4.1.1                  
 [52] gridBase_0.4-7                ellipsis_0.3.2                Rcpp_1.0.7                   
 [55] plyr_1.8.6                    base64enc_0.1-3               sparseMatrixStats_1.4.2      
 [58] progress_1.2.2                zlibbioc_1.38.0               purrr_0.3.4                  
 [61] RCurl_1.98-1.4                prettyunits_1.1.1             viridis_0.6.1                
 [64] cluster_2.1.2                 magrittr_2.0.1                data.table_1.14.0            
 [67] hms_1.1.0                     mime_0.11                     evaluate_0.14                
 [70] xtable_1.8-4                  XML_3.99-0.7                  gridExtra_2.3                
 [73] shape_1.4.6                   compiler_4.1.1                tibble_3.1.4                 
 [76] crayon_1.4.1                  entropy_1.3.0                 R.oo_1.24.0                  
 [79] htmltools_0.5.2               later_1.3.0                   tidyr_1.1.3                  
 [82] howmany_0.3-1                 DBI_1.1.1                     ExperimentHub_2.0.0          
 [85] dbplyr_2.1.1                  MASS_7.3-54                   ade4_1.7-17                  
 [88] cli_3.0.1                     uchardet_1.1.0                R.methodsS3_1.8.1            
 [91] pkgconfig_2.0.3               bigmemory.sri_0.1.3           rncl_0.8.4                   
 [94] registry_0.5-1                locfdr_1.1-8                  signal_0.7-7                 
 [97] IRdisplay_1.0                 xml2_1.3.2                    annotate_1.70.0              
[100] vipor_0.4.5                   rngtools_1.5                  pkgmaker_0.32.2              
[103] XVector_0.32.0                stringr_1.4.0                 digest_0.6.27                
[106] graph_1.70.0                  softImpute_1.4-1              Biostrings_2.60.2            
[109] edgeR_3.34.1                  DelayedMatrixStats_1.14.3     curl_4.3.2                   
[112] kernlab_0.9-29                shiny_1.6.0                   lifecycle_1.0.0              
[115] nlme_3.1-153                  jsonlite_1.7.2                Rhdf5lib_1.14.2              
[118] BiocNeighbors_1.10.0          viridisLite_0.4.0             limma_3.48.3                 
[121] fansi_0.5.0                   pillar_1.6.2                  lattice_0.20-44              
[124] KEGGREST_1.32.0               fastmap_1.1.0                 survival_3.2-13              
[127] interactiveDisplayBase_1.30.0 glue_1.4.2                    png_0.1-7                    
[130] BiocVersion_3.13.1            bit_4.0.4                     stringi_1.7.4                
[133] HDF5Array_1.20.0              blob_1.2.2                    BiocSingular_1.8.1           
[136] AnnotationHub_3.0.1           memoise_2.0.0                 IRkernel_1.2                 
[139] dplyr_1.0.7                   irlba_2.3.3                   ape_5.5  

[gbader]

Hi - we're looking into this. It may be caused by web filtering recently implemented at our university. Could you try changing the URL from http to https in netDx/R/fileCache.R?

[EgoJing]

the url is good for online environment. However, when we are running in the offline environment, downloading is not applicable. Do we have an offline method for this issue?