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Error running netDx vignette 1 locally #85

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writingindy opened this issue Sep 13, 2021 · 2 comments
Open

Error running netDx vignette 1 locally #85

writingindy opened this issue Sep 13, 2021 · 2 comments

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@writingindy
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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
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gbader commented Sep 14, 2021

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
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EgoJing commented Jul 14, 2022

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?

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