Open shraddhapai opened 3 years ago
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.
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.
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.
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
exactly the same issue. How is it now?
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
sessionInfo() Output